Methods of modulating seed and organ size in plants

ABSTRACT

This invention relates to a plant E3 ubiquitin ligase (termed DA2) which acts synergistically with DA1 to control seed and organ size. Methods of increasing plant yield are provided that comprise reducing the expression or activity of DA2 in a plant that is deficient in DA1 expression or activity. Plants with increased yield and methods of producing such plants are also provided.

CROSS REFERENCE TO RELATED APPLICATIONS

This is a Continuation Application of U.S. Ser. No. 16/387,196, filed Apr. 17, 2019, which is a Divisional Application of U.S. Ser. No. 14/912,045 filed Feb. 12, 2016, now U.S. Pat. No. 10,329,577, issued Jun. 25, 2019, which is a U.S. National Phase application claiming priority to PCT/EP2014/066427 filed Jul. 30, 2014, which claims priority to PCT/CN2013/081457 filed Aug. 14, 2013, which are herein incorporated by reference in their entirety.

SEQUENCE LISTING XML

The instant application contains a sequence listing, which has been submitted in XML file format by electronic submission and is hereby incorporated by reference in its entirety. Said XML file, created on Oct. 25, 2022, is named P11740US02.xml and is 145,078 bytes in size.

FIELD OF INVENTION

This invention relates to methods of altering the size of the seeds and organs of plants, for example to improve plant yield.

BACKGROUND OF INVENTION

The size of seeds and organs is an agronomically and ecologically important trait that is under genetic control (Alonso-Blanco, C. PNAS USA 96, 4710-7 (1999); Song, X. J. Nat Genet 39, 623-30 (2007); Weiss, J. Int J Dev Biol 49, 513-25 (2005); Dinneny, J. R. Development 131, 1101-10 (2004); Disch, S. Curr Biol 16, 272-9 (2006); Science 289, 85-8 (2000);Horiguchi, G. Plant J 43, 68-78 (2005); Hu, Y Plant J 47, 1-9 (2006); Hu, Y. Plant Cell 15, 1951-61 (2003); Krizek, B. A. Dev Genet 25, 224-36 (1999);Mizukami, Y. PNAS USA 97, 942-7 (2000); Nath, U. Science 299, 1404-7 (2003);Ohno, C. K. Development 131, 1111-22 (2004); Szecsi, J. Embo J 25, 3912-20 (2006); White, D. W. PNAS USA 103, 13238-43 (2006); Horvath, B. M. Embo J 25, 4909-20 (2006); Garcia, D. Plant Cell 17, 52-60 (2005). The final size of seeds and organs is constant within a given species, whereas interspecies seed and organ size variation is remarkably large, suggesting that plants have regulatory mechanisms that control seed and organ growth in a coordinated and timely manner. Despite the importance of seed and organ size, however, little is known about the molecular and genetic mechanisms that control final organ and seed size in plants.

The genetic regulation of seed size has been investigated in plants, including in tomato, soybean, maize, and rice, using quantitative trait locus (QTL) mapping. To date, in the published literature, two genes (Song, X. J. Nat Genet 39, 623-30 (2007); Fan, C. Theor. Appl. Genet. 112, 1164-1171 (2006)), underlying two major QTLs for rice grain size, have been identified, although the molecular mechanisms of these genes remain to be elucidated. In Arabidopsis, eleven loci affecting seed weight and/or length in crosses between the accessions Ler and Cvi, have been mapped {Alonso-Blanco, 1999 supra}, but the corresponding genes have not been identified. Recent studies have revealed that AP2 and ARF2 are involved in control of seed size. Unfortunately, however, ap2 and arf2 mutants have lower fertility than wild type (Schruff, M.C. Development 137, 251-261 (2006); Ohto, M. A. PNAS USA 102, 3123-3128 (2005); Jofuku, K. D. PNAS USA 102, 3117-3122 (2005)). In addition, studies using mutant plants have identified several positive and negative regulators that influence organ size by acting on cell proliferation or expansion {Krizek, B. A. Dev Genet 25, 224-36 (1999); Mizukami, Y. Proc Natl Acad Sci USA 97, 942-7 (2000); Nath, U. Science 299, 1404-7 (2003); Ohno, C. K. Development 131, 1111-22 (2004); Szecsi, J. Embo J 25, 3912-20 (2006); White, D. W. PNAS USA 103, 13238-43 (2006); Horvath, B. M. Embo J 25, 4909-20 (2006); Garcia, D. Plant Cell 17, 52-60 (2005). Horiguchi, G. Plant J 43, 68-78 (2005); Hu, Y Plant J 47, 1-9 (2006) Dinneny, J. R. Development 131, 1101-10 (2004)).

Several factors involved in ubiquitin-related activities have been known to influence seed size. A growth-restricting factor, DA1, is a ubiquitin receptor and contains two ubiquitin interaction motifs (UIMs) that bind ubiquitin in vitro, and da1-1 mutant forms large seeds by influencing the maternal integuments of ovules (Li et al., 2008). Mutations in an enhancer of da1-1 (EOD1), which encodes the E3 ubiquitin ligase BIG BROTHER (BB) (Disch et al., 2006; Li et al., 2008), synergistically enhance the seed size phenotype of da1-1, indicating that DA1 acts synergistically with EOD1/BB to control seed size. In rice, a quantitative trait locus (QTL) for GRAIN WIDTH AND WEIGHT2 (GW2), encoding an E3 ubiquitin ligase, controls grain size by restricting cell division (Song et al., 2007). A GW2 homologue in wheat has been identifed (Ta-GW2; Bednarek et al 2012). An unknown protein encoded by rice qSW5/GW5 is required to limit grain size in rice (Shomura et al., 2008; Weng et al., 2008). GW5 physically interacts with polyubiquitin in a yeast two-hybrid assay, suggesting that GW5 may be involved in the ubiquitin-proteasome pathway (Weng et al., 2008). However, it is not clear whether these two factors act in maternal and/or zygotic tissues in rice.

Identification of further factors that control the final size of both seeds and organs will not only advance understanding of the mechanisms of size control in plants, but may also have substantial practical applications for example in improving crop yield and plant biomass for generating biofuel.

SUMMARY OF INVENTION

The present inventors have identified a plant E3 ubiquitin ligase (termed DA2) which regulates the final size of seeds and organs by restricting cell proliferation in the integuments of developing seeds. DA2 was unexpectedly found to act synergistically with DA1 and independently of EOD1 to control seed and organ size. The targeting of DA2 and DA1 and/or EOD1 may therefore be useful in improving plant yield.

An aspect of the invention provides a method of increasing the yield of a plant comprising;

reducing the expression or activity of a DA2 polypeptide within cells of the plant,

wherein the plant is deficient in DA1 expression or activity.

Another aspect of the invention provides a method of increasing the yield of a plant comprising;

reducing the expression or activity of a DA2 polypeptide within cells of the plant,

wherein the plant is deficient in EOD1 expression or activity.

Another aspect of the invention provides a method of increasing the yield of a plant comprising;

reducing the expression or activity of a DA2 polypeptide within cells of said plant,

wherein the plant is deficient in DA1 and EOD1 expression or activity.

Another aspect of the invention provides a method of increasing the yield of a plant comprising;

reducing or abolishing the expression or activity of a DA2 polypeptide within cells of said plant, and;

i) reducing or abolishing the expression or activity of a DA1 polypeptide within said cells,

ii) reducing or abolishing the expression or activity of EOD1 within said cells, and/or

iii) expressing a dominant-negative DA polypeptide within said cells.

Another aspect of the invention provides a method of producing a plant with an increased yield comprising:

providing a plant cell that is deficient in the expression or activity of DA1, EOD1 or both DA1 and EOD1,

incorporating a heterologous nucleic acid which abolishes or suppresses the expression or activity of a DA2 polypeptide into the plant cell by means of transformation, and;

regenerating the plant from one or more transformed cells.

BRIEF DESCRIPTION OF DRAWINGS

FIGS. 1A-E show seed and organ size in the da1-1 mutant. FIG. 1A shows the projective area of Col-0, da1-1 and 35S::DA2#1 seeds. The seeds were classified into three groups (>0.13, 0.12-0.13 and <0.12 mm2). Values for each group are expressed as a percentage of the total seed number analyzed. FIG. 1B shows the seed number per silique for Col-0, da1-1 and 35S::DA2#1. Siliques (from the fourth silique to the tenth silique) on main stem were used to measure seed number per silique. FIG. 1C shows seed weight per plant for Col-0, da1-1 and 35S::DA2#1. FIG. 1D shows seed number per plant for Col-0, da1-1 and 35S::DA2#1. FIG. 1E shows the height of Col-0, da1-1 and 35S::DA2#1 plants. Values (FIGS. 1B-E) are given as mean±SE relative to the wild-type value, set at 100%. **, P<0.01 and *, P<0.05 compared with the wild type (Student's t-test).

FIG. 2 shows 4-d-old plants of Col-0 (left), da1-1 (middle) and 35S::DA2#1 (right) and flowers of Col-0 (top), da1-1 (middle) and 35S::DA2#1 (bottom).

FIGS. 3A-D show that DA1 and DA2 act synergistically to control seed size. FIG. 3A shows dry seeds of Col-0, da1-1, da1-1 and da1-1 da1-1. FIG. 3B shows 10-day-old seedlings of Col-0, da1-1, da1-1 and da1-1 da1-1 (from left to right). FIG. 3C shows Seed weight of Col-0, da1-1, da2-1 and da1-1 da2-1. FIG. 3D shows seed weight of Col-0, dal-ko1, da2-1 and da1-ko1 da2-1. Values are given as mean±SE relative to the respective wild-type values, set at 100%. **, P<0.01 and *, P<0.05 compared with the wild type (Student's t-test). Bars: FIG. 3A, 0.1mm; FIG. 3B, lm

FIG. 4 shows that DA1 and DA2 act synergistically to control seed size. Upper left panel shows cotyledon area of 10-day-old Col-0, da1-1, da2-1 and da1-1 da2-1 seedlings. Upper right panel shows cotyledon area of 10-day-old Col-0, da1-ko1, da2-1 and da1-ko1 da2-1 seedlings. Lower left panel shows the average area of palisade cells in cotyledons of Col-0, da1-1, da2-1 and da1-1 da2-1 embryos. Lower right panel shows projective area of Col-0, da1-1,da1-1 da2-1, da1-ko1 da2-1, da1-ko1 dar1-1 and da1-ko1 dar1-1 da2-1 seeds. Values are given as mean±SE relative to the respective wild-type values, set at 100%. **, P<0.01 and *, P<0.05 compared with the wild type (Student's t-test).

FIG. 5 shows that DA1 and DA2 act synergistically to control cell proliferation in maternal integuments of developing seeds. The images show mature Ovules of Col-0, da1-1, da2-1 and da1-1 da2-1. The da2-1 mutation synergistically enhances the ovule size of da1-1.

FIG. 6 shows (left panel) the projective area of Col-0×Col-0 (c/c) F1, da2-1×da2-1 (d2/d2) F1, Col-0×da2-/ (c/d2) F1, and da2-/xCol-0 (d2/c) Fl seeds and (middle panel) the projective area of Col-0xCol-0 (c/c) F1, da1-ko1 da2-1 x da1-ko1 da2-1 (dd/dd) F1, Col-0×da1-ko1 da2-1 (c/dd) F1, da1-ko1 da2-1×Col-0 (dd/c) Fl seeds. Right panel shows projective seed area after pollination of dal-ko1/+da2-1/+plants with da1-ko1 da2-1 double mutant pollen leading to the development of dal-ko1/+da2-1/+(a), dal-ko1/+da2-1da2-1 (b), da1-ko1/da1-ko1 da2-1/+(c) and da1-ko1 da2-1 (d) embryos within dal-ko1/+da2-1/+seed coats. Projective area of individual seeds from dal-ko1/+da2-1/+plants fertilized with da1-ko1 da2-1 double mutant pollen was measured. These seeds were further genotyped for da1-ko1 and da2-1 mutations. The data shows that da1-ko1 and da2-1 mutations are not associated with variation in the size of these seeds (P>0.05, Student's t-test). Values are given as mean±SE relative to the respective wild-type values, set at 100%. **, P<0.01 compared with the wild type (Student's t-test).

FIG. 7 shows (left panel) the projective area of Col-0, da1-1, da2-1 and da1-1 da2-1 mature ovules; (middle panel) the number of cells in the outer integuments of Col-0, da1-1, da2-1 and da1-1 da2-1 seeds at 6 DAP and 8 DAP; and (right panel) the average length of cells in the outer integuments of Col-0, da1-1, da2-1 and da1-lda2-1 seeds at 6 DAP and 8 DAP calculated from the outer integument length and cell number for individual seeds.

FIGS. 8A-B show the DA2 gene and protein structure. FIG. 8A shows the DA2 gene structure. The start codon (ATG) and the stop codon (TAA) are indicated. Closed boxes indicate the coding sequence, open boxes indicate the 5′ and 3′ untranslated regions, and lines between boxes indicate introns. The T-DNA insertion site (da2-1) in the DA2 gene is shown. FIG. 8B shows that the DA2 protein contains a predicted RING domain.

FIG. 9 shows E3 ubiquitin ligase activity of DA2. MBP-DA2 and mutated DA2 (MBP-DA2C59S and MBP-DA2N91L) fusion proteins were assayed for E3 ubiquitin ligase activity in the presence of El, E2 and His-ubiquitin (His-Ub). Ubiquitinated proteins were detected by immunoblotting (IB) with anti-His antibody (Anti-His) and anti-MBP antibody (Anti-MBP), respectively. The lower arrow indicates MBP-DA2 proteins, and the upper arrow shows ubiquitinated MBP-DA2 proteins.

FIG. 10 shows the projective area of Col-0, da2-1, COM#6, COM#8, and COM#/0 seeds (upper panel), where COM is da2-1 transformed with the DA2 coding sequence driven by its own promoter; petal area of Col-0, da2-1, COM#6, COM#8, and COM#/0 plants (middle panel) and quantitative real-time RT-PCR analysis of the DA2 gene expression in Col-0, da2-1, COM#6, COM#8, and COM#/0 seedlings (lower panel). Values are given as mean±SE relative to the da2-1 values, set at 100%. **, P<0.01 compared with the da2-1 mutant (Student's t-test).

FIG. 11 shows expression patterns of DA2. Panel A shows quantitative real-time RT-PCR analysis of the DA2 gene expression. Total RNA was isolated from roots (R), stems (S), leaves (L), seedlings (Se) and inflorescences (In). Panels B-N show DA2 expression activity monitored by pDA2: GUS transgene expression. Four GUS-expressing lines were observed, and all showed a similar pattern, although they differed slightly in the intensity of the staining. Histochemical analysis of GUS activity in a 4-d-old seedling (panel B), a 10-d-old seedling (panel C), a floral inflorescence (panel D), the developing petals (panels E-G), the developing stamens (panels H-I), the developing carpels (panels J-L), and the developing ovules (panels M and N) Bars: panels B-D, 1mm; panels E-N, 0.1mm.

FIG. 12 shows that DA1 directly interacts with DA2 in vitro. GST-DA1, GST-DA1R358K, GST-DA1-UIM, GST-DA1-LIM, GST-DA1-LIM+C and GST-DA1-C were pulled down (PD) by MBP-DA2 immobilized on amylose resin and analyzed by immunoblotting (IB) using an anti-GST antibody.

FIG. 13 shows a schematic diagram of DA1 and its derivatives containing specific protein domains. The predicted DA1 protein contains two UIM motifs, a single LIM domain and the C-terminal region.

FIG. 14 shows that DA1 interacts with DA2 in vivo. Nicotiana benthamiana leaves were transformed by injection of Agrobacterium tumefaciens GV3101 cells harbouring 35S:Myc-DA1 and 35S:GFP-DA2 plasmids. Total proteins were immunoprecipitated with GFP-Trap-A, and the immunoblot was probed with anti-GFP and anti-Myc antibodies, respectively. Myc-DA1 was detected in the immunoprecipitated GFP-DA2 complex, indicating that there is a physical association between DA1 and DA2 in planta.

FIGS. 15A-E show that da2-1 mutants display increased organ size. FIG. 15A shows petal length (PL), petal width (PW), petal area (PA), sepal area (SA), carpel length (CL), long stamen length (LSL) and short stamen length (SSL) of Col-0, da2-1 and 35S:DA2#1 plants. FIG. 15B shows fifth leaf area of Col-0, da2-1 and 35S:DA2#1 plants. FIG. 15C shows weight of Col-0, da2-1 and 35S:DA2#1 flowers. FIG. 15D shows the size of adaxial epidermal cells in the maximal width region of Col-0 and da2-1 petals. FIG. 15E shows the size of palisade cells in the fifth leaves of Col-0 and da2-1. The opened flowers (stage 14) were used to measure the size of petals, flower weight and the size of epidermal cells. Values are given as mean±SE relative to the respective wild-type values, set at 100%. **, P<0.01 compared with the wild type (Student's t-test).

FIGS. 16A-D show that DA1 and DA2 act synergistically to control seed size. FIG. 16A shows the petal area of Col-0, da1-kol, da2-1 and da1-kolda2-1 flowers. FIG. 16B shows the size of adaxial epidermal cells in the maximal width region of Col-0, da1-kol, da2-1 and da1-kolda2-1 petals. FIG. 16C shows seed weight of Col-0, eodl-2, da2-1 and eod1-2 da2-1. FIG. 16D shows petal area of Col-0, eod1-2, da2-1 and eod1-2 da2-1. The opened flowers (stage 14) were used to measure the size of petals and the size of epidermal cells. Values are given as mean±SE relative to the respective wild-type values, set at 100%. **, P<0.01 and *, P<0.05 compared with the wild type (Student's t-test). Bar: 0.1mm.

FIG. 17 shows that overexpression of DA2 restricts organ growth. The left panel shows that petal area of Col-0, 35S:DA2#2 and 35S:DA2#4. The right panel shows expression levels of DA2 in Col-0, 35S:DA2#2 and 35S:DA2#4 seedlings. Values are given as mean±SE relative to Col-0 values, set at 100%. **, P<0.01 compared with the wild type (Student's ttest).

FIGS. 18A-C show that overexpression of DA2L restricts organ growth. FIG. 18A shows 20-day-old plants of Col-0, 35S:DA2L#1, 35S:DA2L#3, 35S:DA2L#4, 35S:DA2L#5, and 35S:DA2L#6. FIG. 18B shows 30 -day-old plants of Col-0, 35S:DA2L#1, 35S:DA2L#3, 35S:DA2L#4, 35S:DA2L#5, and 35S:DA2L#6. FIG. 18C shows RT-PCR analysis of DA2L expression in Col-0, 35S:DA2L#1, 35S:DA2L#3, 35S:DA2L#4, 35S:DA2L#5 and 35S:DA2L#6 seedlings. RT-PCR was performed on first-strand cDNA prepared from 2-week-old seedlings. cDNA was standardized by reference to an ACTIN2 standard. Bars: FIG. 18A, 1cm, FIG. 18B, 1cm

FIGS. 19A-C show that overexpression of GW2 restricts seed and organ growth. FIG. 19A shows 30 -day-old plants of Col-0, 35S:GW2#1, 35S:GW2#2, 35S:GW2#3, 35S:GW2#6 and 35S:GW2L#7. FIG. 19B shows projective area of Col-0, 35S:GW2#1, 35S:GW2#2, 35S:GW2#3, 35S:GW2#6 and 35S:GW2L#7 seeds. FIG. 19C shows quantitative real-time RT-PCR analysis of the GW2 gene expression in Col-0, 35S:GW2#1, 35S:GW2#2, 35S:GW2#3, 35S:GW2#6 and 35S:GW2L#7 seedlings. Values (FIG. 19B) are given as mean±SE relative to Col-0 values, set at 100%. **, P<0.01 compared with the wild type (Student's t-test). Bar: FIG. 19A, 1cm

DETAILED DESCRIPTION OF EMBODIMENTS OF THE INVENTION

This invention relates to methods of altering plant traits which affect yield, such as seed and organ size, by altering the expression or activity of the plant E3 ubiquitin ligase DA2 in combination with the alterations in the expression or activity of DA1 and/or EOD1. Preferably, the expression or activity of DA2 and DA1 is altered in the plant.

The expression or activity DA2 expression may be altered before, at the same time, or after alteration of DA1 and/or EOD1 expression or activity. For example, in some embodiments, the expression or activity of a DA2 polypeptide may be altered in one or more plant cells which already have one of; altered DA1 expression or activity, altered EOD1 expression or activity, or altered DA1 and EOD1 expression or activity.

Provided herein are methods of increasing the yield of plant, for example by increasing organ or seed size, that comprise providing a plant that is deficient in DA1 and/or EOD1 expression or activity and reducing the expression of DA2 in one or more cells of the plant. In other embodiments, the expression or activity of DA1 and/or EOD1 may be reduced in one or more plant cells which have reduced expression or activity of a DA2 polypeptide.

Other methods may comprise reducing the expression of DA2 in one or more cells of the plant and reducing the expression or activity of DA1, EOD1 or both DA1 and EOD1 in one or more cells.

Also provided herein are methods of producing a plant with increased yield relative to wild-type plant that comprise;

(a) incorporating into a plant cell by means of transformation

-   -   (i) a first heterologous nucleic acid which reduces the         expression of a DA2 polypeptide,     -   (ii) a second heterologous nucleic acid which reduces the         expression of one of a DA1 polypeptide and a EOD1 polypeptide,         and optionally,     -   (iii) a third heterologous nucleic acid which reduces the         expression of the other of a DA1 polypeptide and a EOD1         polypeptide, and

(b) regenerating the plant from one or more transformed cells.

Other methods of producing a plant with increased yield may comprise:

providing a plant cell that is deficient in DA1 and/or EOD1 expression or activity, preferably DA1 activity,

incorporating a heterologous nucleic acid which reduces the activity or expression of a DA2 polypeptide into the plant cell by means of transformation, and;

regenerating the plant from the transformed cell.

Following regeneration, a plant with reduced activity or expression of a DA2 polypeptide and reduced activity or expression of DA1 and/or EOD1 relative to the wild type plant may be selected.

The combination of reduced DA2 expression and reduced DA1 and/or EOD1 expression synergistically increase the size of the seeds and/or organs of the plant, thereby increasing the plant yield.

One or more yield-related traits in the plant may be improved by the combination of reduced DA2 expression or activity and reduced DA1 and/or EOD1 expression or activity. For example, one or more of life-span, organ size and seed size may be increased in the plant relative to control or wild-type plants in which expression of the DA2 polypeptide has not been reduced.

Expression or activity of DA2, DA1 or EOD1 may be reduced in the methods described herein by at least 50% relative to the wild-type plant, at least 60%, at least 70%, at least 80%, at least 90%, at least 95% or at least 98%. In some preferred embodiments, expression or activity is reduced to zero or substantially zero (i.e. expression or activity is abolished).

Methods of the invention comprise altering the expression or activity of a DA2 polypeptide in one or more cells of a plant.

DA2 polypeptides are E3 ubiquitin ligases found in plants. DA2 polypeptides whose expression or activity is reduced as described herein may comprise a RING domain (Stone, S.L. et al. (2005)), preferably a C5HC2, C5NC2 or C5TC2 RING domain. A suitable RING domain may consist of the amino acid sequence of SEQ ID NO: 1;

(SEQ ID NO: 1) C(X)₂C(X)₁₁CC(X)₄CX2CX₇(H/N/T)X₆CX₂C.

For example, a suitable RING domain may consist of the amino acid sequence of SEQ ID NO: 2;

(SEQ ID NO: 2) CPICFL(Y/F)YPSLNRS(K/R)CC(S/M/T/A)K(G/S)ICTECFL (Q/R)MK(P/N/S/V/T/N)(T/P)(H/N/T)(T/S)(A/T/C) (R/Q/K)PTQCP(F/Y)C

In some embodiments, the H/N/T residue at position 33 in the RING domain of SEQ ID NO: 2 may be T or N.

In some preferred embodiments, a DA2 polypeptide may comprise a RING domain having an amino acid sequence shown in Table 1 (SEQ ID NOS: 3-19), for example Arabidopsis DA2 (SEQ ID NO: 11), Arabidopsis DAL2 (SEQ ID NO: 13) or Rice GW2 (SEQ ID NO: 7) or a variant thereof. For example a RING domain may have the amino acid sequence of residues 59 to 101 of SEQ ID NO: 20 (PT_GI-224061326.pro), residues 59 to 101 of SEQ ID NO: 21 (Rc_GI-255578534.pro), residues 59 to 101 of SEQ ID NO: 22 (Vv_GI-147817790,pro), residues 59 to 101 of SEQ ID NO: 23 (Gm_GI-356549538_(T)ro), residues 59 to 101 of SEQ ID NO: 24 (At_GI-18411948.pro), residues 61 to 103 of SEQ ID NO: 25 (Ta_GI 408743661.pro), residues 61 to 103 of SEQ ID NO: 26(Hv_GI-1641.371454..pro), residues 61 to 103 of SEQ ID NO: 27 (Bd_GI-357140854.pro), residues 62 to 104 of SEQ ID NO: 28 (Os_GI-115445269.pro), residues 63 to 105 of SEQ ID NO: 29 (Sb_GI-242064618.pro), residues 65 to 107 of SEQ ID NO: 30 (Zm_GI-220961719.pro), residues 61 to 103 of SEQ ID NO: 31 (Ta_GI-408743658_(T)ro), residues 43 to 85 of SEQ ID NO: 32 (Bd_GI-357125256.pro), residues 62 to 104 of SEQ ID NO: 33 (Os_GI-218197613.pro), residues 62 to 104 of SEQ ID NO: 34 (Zm_GI-260935347.pro) or residues 62 to 104 of SEQ ID NO: 35 (Sb_GI-242092026_(T)ro).

Further suitable RING domain sequences may be identified using standard sequence analysis techniques as described herein (e.g. Simple Modular Architecture Research Tool (SMART); EMBL Heidelberg, DE).

DA2 polypeptides may further comprise a first consensus domain. The first consensus domain may be located upstream (i.e. on the N terminal side) of the RING domain. A suitable first consensus domain may consist of the amino acid sequence of SEQ ID NO: 36.

(SEQ ID NO: 36) Q(Q/Absent)GLY(P/M/N/V/Q/L/V/E)(H/S/N)(P/K/R)D (I/V)D(L/T/H/V/Q)(K/R)KL(R/K)(R/K)LI(V/L)(E/D) (A/S/T)KLAPC

In some preferred embodiments, a DA2 polypeptide may comprise a first consensus domain of a DA2 amino acid sequence shown in Table 2, for example residues 20 to 45 of SEQ ID NO: 20, residues 20 to 45 of SEQ ID NO: 21, residues 20 to 45 of SEQ ID NO: 22, residues 20 to 45 of SEQ ID NO: 23, residues 20 to 45 of SEQ ID NO: 24, residues 21 to 46 of SEQ ID NO: 25, residues 21 to 46 of SEQ ID NO: 26, residues 21 to 46 of SEQ ID NO: 27, residues 21 to 46 of SEQ ID NO: 28, residues 21 to 46 of SEQ ID NO: 29,residues 21 to 46 of SEQ ID NO: 30, residues 21 to 46 of SEQ ID NO: 31, residues 4 to 29 of SEQ ID NO: 32, residues 23 to 48 of SEQ ID NO: 33, residues 23 to 48 of SEQ ID NO: 34 or residues 23 to 48 of SEQ ID NO: 35.

A DA2 polypeptide may further comprise a second consensus domain. The second consensus domain may be located downstream (i.e. on the C terminal side) of the RING domain. The second consensus domain may consist of the amino acid sequence of SEQ ID NO: 37.

(SEQ ID NO: 37) (N/S)YAVEYRG(V/G)K(T/S)KEE(K/R)(G/S)(V/T/I/F/L/M) EQ(L/I/V/F)EEQ(R/L/K)VIEA(Q/K)(I/M)RMR(H/Q)(K/Q) (E/A).

In some preferred embodiments, a DA2 polypeptide may comprise a second consensus domain of an DA2 amino acid sequence shown in Table 2, for example residues 106 to 141 of SEQ ID NO: 20, residues 106 to 141 of SEQ ID NO: 21, residues 106 to 141 of SEQ ID NO: 22, residues 106 to 141 of SEQ ID NO: 23, residues 106 to 141 of SEQ ID NO: 24, residues 107 to 143 of SEQ ID NO: 25, residues 107 to 143 of SEQ ID NO: 26, residues 107 to 143 of SEQ ID NO: 27, residues 108 to 144 of SEQ ID NO: 28, residues 109 to 145 of SEQ ID NO: 29, residues 111 to 147 of SEQ ID NO: 30, residues 107 to 143 of SEQ ID NO: 31, residues 90 to 125 of SEQ ID NO: 32, residues 108 to 143 of SEQ ID NO: 33, residues 108 to 143 of SEQ ID NO: 34 or residues 108 to 143 of SEQ ID NO: 35.

Further examples of suitable first and second domain sequences may be identified using standard sequence analysis techniques as described herein (e.g. Simple Modular Architecture Research Tool (SMART); EMBL Heidelberg, DE).

In some preferred embodiments, a DA2 polypeptide whose expression or activity is reduced as described herein may comprise a RING Domain of SEQ ID NO: 2, first consensus domain of SEQ ID NO: 36 and a second consensus domain of SEQ ID NO: 37.

For example, a DA2 polypeptide may comprise any combination of RING domain sequence, first consensus domain sequence and second consensus domain sequence as set out above.

A suitable DA2 polypeptide may comprise an amino acid sequence of any one of SEQ ID NOS 20 to 35 as set out in Table 2 or may be variant of one of these sequences. In some preferred embodiments, a DA2 polypeptide may comprise the amino acid sequence of SEQ ID NO: 28 or 33 (OsGW2), SEQ ID NO: 24 (AtDA2), SEQ ID NO: 25 or SEQ ID NO: 31 (TaGW2) or may be a variant of any one of these sequences which has E3 ubiquitin ligase activity.

A DA2 polypeptide which is a variant of any one of SEQ ID NOS: 20 to 35 or other reference DA2 sequence may comprise an amino acid sequence having at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 98% sequence identity to the reference DA2 sequence.

A DA2 polypeptide which is a variant of any one of SEQ ID NOS: 20 to 35 may further comprise a RING domain having the sequence of SEQ ID NO: 2 a first consensus domain having the sequence of SEQ ID NO: 36 and a second consensus domain having the sequence of SEQ ID NO: 37. Examples of suitable sequences are set out above. In some preferred embodiments, a DA2 polypeptide may comprise the RING domain, first consensus domain and second consensus domain of any one of SEQ ID NOS: 20 to 35.

A nucleic acid encoding a DA2 polypeptide may comprise a nucleotide sequence set out in a database entry selected from the group consisting of JN896622.1 GI:408743658 (TaGW2-A); and JN896623.1 GI:408743660 (TaGW2-B) or may be variant of one of these sequences.

In some preferred embodiments, a nucleic acid encoding a DA2 polypeptide may comprise the nucleotide sequence encoding AtDA2, AtDAL2, OsGW2, TaGW2-A or TaGW2-B or may be a variant of any one of these DA2 sequences which encodes a polypeptide which has DA2 activity.

DA2 polypeptides and encoding nucleic acids may be identified in any plant species of interest, in particular a crop plant, such as wheat, barley, maize, rice, soybean, and another agricultural plants, using routine sequence analysis techniques.

Reduction in DA2 expression or activity in a plant is shown herein to synergistically enhance the effect on yield-associated traits in plants of mutations that reduce the activity or expression of DA1. In preferred embodiments, methods described herein may comprise reducing DA2 expression in a plant that is deficient in DA1 expression or activity or reducing both DA1 and DA2 expression in a plant.

DA1 polypeptides are ubiquitin receptors found in plants and are described in detail in Li et al (2008), Wang, et al (2012) and WO2009/047525. DA1 polypeptides whose expression or activity is reduced as described herein may comprise a LIM domain, a conserved C terminal domain and one or more UIM domains.

A LIM domain comprises two Zn finger motifs and may have the amino acid sequence(SEQ ID NO:38);

C(X)₂C(X)₁₆₋₂₃(H/C)(X)_(2/4)(C/H/E)(X)₂C(X)₂C(X)₁₄₋₂₁(C/H) (X)_(2/1/3)(C/H/D/E)X where X is any amino acid and Zn coordinating residues are underlined.

The Zn coordinating residues in the LIM domain may be C, H, D or E, preferably C.

In some preferred embodiments, a LIM domain may comprise CXXC, HXXCXXCXXC and HxxC motifs, where X is any amino acid. For example, a LIM domaim may comprise the amino acid sequence (SEQ ID NO:39);

C(X)₂C(X)₁₆₋₂₃(H)(X)₃₂(C)(X)₂C(X)₁₄₋₂₁H(X)₂CX

where X is any amino acid and Zn coordinating residues are underlined

In some embodiments, a LIM domain may comprise the amino acid sequence of the AtDA1 LIM domain;

CAGCNMEIGHGRFLNCLNSLWHPECFRCYGCSQPISEYEFSTSGNYPFH KACY (SEQ ID NO: 40; Zn coordinating residues are underlined)

Other LIM domains include the LIM domain of an DA1 amino acid sequence shown in Table 3, for example residues 141 to 193 of SEQ ID NO: 41 (Si_GI-514815267.pro), residues 123 to 175 of SEQ ID NO: 42 (Bd_GI-357157184.pro), residues 155 to 207 of SEQ ID NO: 43(Br_DA1b.pro), residues 172 to 224 of SEQ ID NO: 44 (Br_DA1a.pro), residues 172 to 224 of SEQ ID NO: 45 (At_GI-15221983,pro), residues 117 to 169 of SEQ ID NO: 46 (Te_GI-508722773,pro), residues 117 to 169 of SEQ ID NO: 47 (Gm_GI-356564241.pro), residues 121 to 173 of SEQ ID NO: 48 (Gm_GI-356552145.pro), residues 119 to 171 of SEQ ID NO: 49 (Vv_GI-302142429,pro), residues 122 to 174 of SEQ ID NO: 50 (Vv_GI-359492104,pro), residues 125 to 177 of SEQ ID NO: 51 (Sl_GI-460385048,pro), residues 516 to 568 of SEQ ID NO: 52 (Os_GI-218197709.pro), residues 124 to 176 of SEQ ID NO: 53 (Os_GI-115466772,pro), residues 150 to 202 of SEQ ID NO: 54 (Bd_GI-357160893.pro), residues 132 to 184 of SEQ ID NO: 55 (Bd_GI-357164660.pro), residues 124 to 176 of SEQ ID NO: 56 (Sb_GI-242092232,pro), residues 147 to 199 of SEQ ID NO: 57 (Zm_GI-212275448,pro), residues 190 to 242 of SEQ ID NO: 58 (At_GI-240256211.pro), residues 162 to 214 of SEQ ID NO: 59 (At_GI-145360806.pro), residues 1240 to 1291 of SEQ ID NO: 60 (At_GI-22326876.pro), residues 80 to 122 of SEQ ID NO: 61 (At_GI-30698242.pro), residues 347 to 402 of SEQ ID NO: 62 (At_GI-30698240.pro), residues 286 to 341 of SEQ ID NO: 63 (At_GI-15240018.pro) or residues 202 to 252 of SEQ ID NO: 64 (At_GI-334188680.pro)

LIM domain sequences may be identified using standard sequence analysis techniques (e.g. Simple Modular Architecture Research Tool (SMART); EMBL Heidelberg, DE).

In addition to a LIM domain, a DA1 protein may further comprise a carboxyl terminal region having an amino acid sequence at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 98% amino acid identity to the sequence of residues 198 to 504 of SEQ ID NO: 41, residues 180 to 487 of SEQ ID NO: 42, residues 212 to 514 of SEQ ID NO: 43, residues 229 to 532 of SEQ ID NO: 44, residues 229 to 532 of SEQ ID NO: 45, residues 174 to 478 of SEQ ID NO: 46, residues 174 to 474 of SEQ ID NO: 47, residues 178 to 478 of SEQ ID NO: 48, residues 176 to 462 of SEQ ID NO: 49, residues 179 to 482 of SEQ ID NO: 50, residues 182 to 486 of SEQ ID NO: 51, residues 573 to 878 of SEQ ID NO: 52, residues 181 to 486 of SEQ ID NO: 53, residues 207 to 512 of SEQ ID NO: 54, residues 189 to 491 of SEQ ID NO: 55, residues 181 to 486 of SEQ ID NO: 56, residues 204 to 508 of SEQ ID NO: 57, residues 247 to 553 of SEQ ID NO: 58, residues 219 to 528 of SEQ ID NO: 59, residues 1296 to 1613 of SEQ ID NO: 60, residues 128 to 450 of SEQ ID NO: 61, residues 404 to 702 of SEQ ID NO: 62, residues 343 to 644 of SEQ ID NO: 63 or residues 256 to 587 of SEQ ID NO: 64.

The carboxyl terminal region of the DA1 protein may comprise the metallopeptidase motif HEMMH (SEQ ID NO: 65).

The carboxyl terminal region may further comprise a EK(X)₈R(X)₄SEEQ (SEQ ID NO: 66) or EK(X)₈R(X)₄SEQ (SEQ ID NO: 67) motif positioned between the LIM domain and HEMMH motif.

In addition to a LIM domain and a conserved carboxyl terminal region, a DA1 protein may comprise a UIM1 domain and a UIM2 domain. The UIM1 and UIM2 domains may be located between the N terminal and the LIM domain of the DA1 protein.

A UIM1 domain may consist of the sequence of p---pLpbAl pb.Sbp-.pp p and a UIM2 domain may consist of the sequence of p---pLpbAl pb.Sbp-spp p wherein;

p is a polar amino acid residue, for example, C, D, E, H, K, N, Q, R, S or T;

b is a big amino acid residue, for example, E, F, H, I, K, L, M, Q, R, W or Y;

s is a small amino acid residue, for example, A, C, D, G, N, P, S, T or V;

1 is an aliphatic amino acid residue, for example, I, L or V;

. is absent or is any amino acid, and

- is any amino acid.

Further examples of UIM1 and UIM2 domain sequences may be identified using standard sequence analysis techniques as described herein (e.g. Simple Modular Architecture Research Tool (SMART); EMBL Heidelberg, DE).

In some preferred embodiments, a DA1 polypeptide may comprise;

a LIM domain of SEQ ID NO: 39,

a C terminal region having at least 20% sequence identity to residues 229 to 532 of SEQ ID NO: 45 or the equivalent region of any one of SEQ NOS 41 to 44 or 46 to 64, as set out above and comprising a EK(X)₈R(X)₄SEEQ or EK(X)₈R(X)₄SEQ motif and a HEMMH motif,

a UIM domain of SEQ ID NO:66, and

a UIM domain of SEQ ID NO:67.

A DA1 protein may comprise an amino acid sequence of a plant DA1 protein shown in Table 3 (SEQ ID NOS: 41 to 64) or may be a homologue or variant of one of these sequences which has DA1 activity. For example, a DA1 polypeptide may comprise an amino acid sequence shown in Table 3 (SEQ ID NOS: 41 to 64) or may be variant of one of these sequences which has DA1 activity.

For example, a DA1 polypeptide may comprise an amino acid sequence of AtDA1, AtDAR1, AtDAR2, AtDAR3, AtDAR4, AtDAR5, AtDAR6, AtDAR7, BrDA1a, BrDA1b, BrDAR1, BrDAR2, BrDAR3-7, BrDAL1, BrDAL2, BrDAL3, OsDA1, OsDAR2, OsDAL3, OsDAL5, PpDAL1, PpDAL2, PpDAL3, PpDAL4, PpDAL5, PpDAL6, PpDAL7, PpDAL8, SmDAL1, SmDAL2 or ZmDA1, preferably AtDA1, AtDAR1 BrDA1a, BrDA1b, OsDA1 or ZmDA1 or a homologue or variant of one of these sequences.

In some preferred embodiments, a DA1 polypeptide may comprise the amino acid sequence of AtDA1 (AT1G19270; NP_173361.1 GI: 15221983) or may be variant of this sequence which has DA1 activity.

Other DA1 protein sequences which include the characteristic features set out above may be identified using standard sequence analysis tools. A skilled person is readily able to identify nucleic acid sequences encoding DA1 proteins in any plant species of interest.

A DA1 protein in a plant species of interest may have an amino acid sequence which is a variant of a DA1 protein reference amino acid sequence set out herein.

A DA1 polypeptide which is a variant of a reference DA1 sequence, such as any one of SEQ ID NOS 41 to 64, may comprise an amino acid sequence having at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 98% sequence identity to the reference sequence.

Particular amino acid sequence variants that occur in a plant species may differ from a reference sequence set out herein by insertion, addition, substitution or deletion of 1 amino acid, 2, 3, 4, 5-10, 10-20 20-30, 30-50, or more than 50 amino acids.

In some embodiments, a DA1 polypeptide which is a variant of the AtDA1 sequence of SEQ ID NO: 45 may comprise a UIM1 domain having the sequence QENEDIDRAIALSLLEENQE (SEQ ID NO: 70) and a UIM2 domain having the sequence DEDEQIARALQESMVVGNSP (SEQ ID NO: 71).

A DA1 polypeptide which is a variant of AtDA1 sequence of SEQ ID NO: 45 may comprise a LIM domain having the sequence:

(SEQ ID NO: 72) ICAGCNMEIGHGRFLNCLNSLWHPECFRCYGCSQPISEYEFSTSGNYPF HKAC

A nucleic acid encoding a DA1 polypeptide may comprise a nucleotide sequence set out in a database entry selected from the group consisting of NM_101785.3 GI:42562170 (AtDA1); NM_001057237.1 GI:115454202 (0sDA1); BT085014.1 GI: 238008663 (ZmDA1) or may be variant of one of these sequences which encodes an active DA1 polypeptide.

In some preferred embodiments, a nucleic acid encoding a DA1 polypeptide may comprise the nucleotide sequence of AtDA1 (NM_101785.3 GI: 42562170), ZmDA1 (BT085014.1 GI: 238008663), OsDA1 (NM_001057237.1 GI:115454202) or may be a variant of any one of these sequences which encodes a polypeptide which retains DA1 activity.

DA1 polypeptides and encoding nucleic acids may be identified in plant species, in particular crop plants, such as wheat, barley, maize, rice, and another agricultural plants, using routine sequence analysis techniques.

In some preferred embodiments, DA1 activity in one or more cells of a plant may be reduced by expression of a dominant-negative DA1 polypeptide in the one or more cells (see for example Li et al (2008); WO2009/047525; Wang et al 2012). A plant expressing a dominant-negative DA1 polypeptide may have a da1-1 phenotype.

A dominant negative allele of a DA1 polypeptide may comprise a DA1 polypeptide having a mutation, e.g. a substitution or deletion, at a a conserved R residue that is located at position 358 of the A. thaliana DA1 amino acid sequence, position 333 of the Z. mays DA1 amino acid sequence or the equivalent position in another DA1 amino acid sequence. For example, a dominant negative allele of a DA1 polypeptide may comprise a mutation of the conserved R residue at a position equivalent to position 358 of the A. thaliana DA1 amino acid sequence or position 333 of the Z mays DA1 amino acid sequence. In preferred embodiments, the conserved R residue may be substituted for K.

The conserved R residue that is located at a position in a DA1 amino acid sequence which is equivalent to position 358 of SEQ ID NO: 45 of A. thaliana DA1 or position 333 of the Z. mays DA1 of SEQ ID NO: 57 is located at the position within the DA1 amino acid sequence which corresponds to R333 of SEQ ID NO:57 and R358 of SEQ ID NO:45 i.e. it is in the same position relative to to the other motifs and domains of the DA1 protein. The conserved R residue is located between the LIM domain and the HEMMH peptidase motif of the C terminal region and is completely conserved in the same sequence context in DA1 proteins. The conserved R residue may be contained in a EK(X)₈R(X)₄SEEQ (SEQ ID NO: 66) or EK(X)₈R(X)₄SEQ (SEQ ID NO: 67) motif within the C terminal region.

The conserved R residue may be identified by aligning these conserved C terminal regions using standard sequence analysis and alignment tools and is identified with an arrow in the sequences of Table 3.

Nucleic acid which encodes a dominant negative allele of a DA protein may be produced by any convenient technique. For example, site directed mutagenesis may be employed on a nucleic acid encoding a DA1 polypeptide to alter the conserved R residue at the equivalent position to R358 of A. thaliana DA1 or R333 of the Zea mays DA1, for example to K. Reagents and kits for in vitro mutagenesis are commercially available.

In some embodiments, a nucleic acid encoding a dominant-negative DA1 polypeptide as described herein may be operably linked to a heterologous regulatory sequence, such as a promoter, for example a constitutive, inducible, tissue-specific or developmental specific promoter. The nucleic acid encoding the dominant-negative DA1 polypeptide may be comprised in one or more vectors. For example, the mutated nucleic acid encoding the dominant-negative allele of a DA1 protein may be further cloned into an expression vector and expressed in plant cells as described below to alter the plant phenotype.

In other embodiments, a mutation may be introduced into an endogenous DA1 nucleic acid in a plant, such that the DA1 polypeptide encoded by the mutant DA1 nucleic acid has dominant-negative activity.

Nucleic acid encoding a dominant-negative DA1 polypeptide may be expressed in the same plant species or variety from which it was originally isolated or in a different plant species or variety (i.e. a heterologous plant).

Reduction or abolition of DA2 expression in a plant is also shown herein to enhance the effect of mutations that reduce the expression or activity of EOD1 on yield-associated traits in plants.

Methods described herein may comprise reducing DA2 expression or activity in a plant that is deficient in EOD1 expression or activity or reducing both DA2 and EOD1 expression or activity in a plant. In preferred embodiments, the plant may also be deficient in DA1 activity or the method may additionally comprise reducing or abolishing DA1 expression in the plant

EOD1 polypeptides are E3 ubiquitin ligases found in plants and are described in detail in Disch et al. (2006), Li et al (2008) and WO2009/047525. An EOD1 polypeptide whose expression or activity is reduced as described herein may comprise an EOD domain. A suitable EOD domain may consist of the amino acid sequence of SEQ ID NO: 73;

(SEQ ID NO: 73) (E/K)RCVICQ(L/M)(K/R/G/T/E)Y(K/R)(R/I)(G/K)(D/N/E) (R/Q/K/L)Q(I/M/V)(K/N/T/A)L(L/P)C(K/S)H(V/A)YH(S/ T/G/A)(E/Q/D/S/G)C(I/G/T/V)(S/T)(K/R)WL(G/T/S)INK (V/I/A/K)CP(V/I)C 

In some preferred embodiments, an EOD1 polypeptide may comprise a EOD domain having an amino acid sequence of residues 195 to 237 of SEQ ID NO: 74 (Zn_GI-22397392:3.pro), residues 195 to 237 of SEQ ID NO: 75 (Sb_GI-242042045.pro), residues 195 to 237 of SEQ ID NO: 76 (Zm_GI-226496789.pro), residues 218 to 260 of SEQ ID NO: 77 (Os_GI-222624282.pro), residues 196 to 238 of SEQ ID NO: 78 (Os-GI-11545104.5.pro), residues 197 to 239 of SEQ ID NO: 79(Bd JiI-357113826.pro), residues 193 to 235 of SEQ ID NO: 80 (Sl_GI-460410949.pro), residues 187 to 229 of SEQ ID NO: 81 (Rc_GI-255582236.pro), residues 150 to 192 of SEQ ID NO: 82 (Pt_GL-224059640.pro), residues 194 to 236 of SEQ ID NO: 83 (Gm_GI-356548935,pro), residues 194 to 236 of SEQ ID NO: 84 (Gm)GI-356544176.pro), residues 194 to 236 of SEQ ID NO: 85 (Vv_GI-359487286.pro), residues 189 to 231 of SEQ ID NO: 86 (Tc_GI-508704801,pro), residues 192 to 234 of SEQ ID NO: 87 (Pp_GI-462414664.pro), residues 190 to 232 of SEQ ID NO: 88 (Cr_GI-482561003.pro), residues 195 to 237 of SEQ ID NO: 89 (At_GI-22331928,pro) or residues 195 to 237 (Sl_GI-460370551.pro) of SEQ ID NO: 90, as shown in Table 4.

Further suitable EOD domain sequences may be identified using standard sequence analysis techniques as described herein (e.g. Simple Modular Architecture Research Tool (SMART); EMBL Heidelberg, DE).

A EOD1 polypeptide whose expression or activity is reduced as described herein may comprise an amino acid sequence of any one of SEQ ID NOS 74 to 90 as set out in Table 4. In some preferred embodiments, a EOD1 polypeptide may comprise the amino acid sequence of SEQ ID NO: 89 (AtEOD1) or SEQ ID NOS: 77 or 78 (OsEOD1) or may be a variant of this sequence which retains E3 ubiquitin ligase activity.

A EOD1 polypeptide which is a variant of any one of SEQ ID NOS: 74 to 90 or other reference EOD1 sequence may comprise an amino acid sequence having at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 98% sequence identity to the reference EOD1 sequence.

A EOD polypeptide which is a variant of any one of SEQ ID NOS: 74 to 90 may further comprise a EOD domain having the sequence of SEQ ID NO: 73. Examples of suitable sequences are set out above.

A nucleic acid encoding a EOD1 polypeptide may comprise a nucleotide sequence set out in a database entry selected from the group consisting of XM_002299911.1 GI:224059639 (PtEOD1); XM_002531864.1 GI:255582235 (RcEOD1); XM_002279758.2 GI:359487285 (VvEOD1); XM_003542806.1 GI:356548934 (GmEOD1a); XM_003540482.1 GI:356544175 (GmEOD1b); XM_002468372.1 GI:242042044 (SbEOD1); NM_001147247.1 GI:226496788 (ZmEOD1); or NP_001030922.1 GI: 79316205 (AtEOD1; At3g63530) or may be variant of one of these sequences.

In some preferred embodiments, a nucleic acid encoding a EOD1 polypeptide may comprise the nucleotide sequence encoding AtEOD1 or OsEOD1 or may be a variant of any one of these sequences which encodes a polypeptide which has EOD1 activity.

EOD1 polypeptides and encoding nucleic acids whose expression or activity is reduced as described herein may be readily identified in any plant species of interest, in particular a crop plant, such as wheat, barley, maize, rice, and another agricultural plants, using routine sequence analysis techniques.

DA2 mutation in plants is also shown herein to synergistically enhance the effect of combinations of DA1 and EOD1 mutations on yield-associated traits in plants.

The methods described herein are not limited to particular plant species and expression or activity of DA2, DA1 and/or EOD1 may be reduced in any plant species of interest, as described herein.

An DA1, DA2 or EOD1 polypeptide in a plant species of interest may have an amino acid sequence which is a variant of a respective DA1, DA2 or EOD1 reference amino acid sequence set out herein. A DA1, DA2 or EOD1 polypeptide which is a variant of a reference sequence set out herein, may comprise an amino acid sequence having at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 98% sequence identity to the reference sequence.

Particular amino acid sequence variants that occur in a plant species may differ from a reference sequence set out herein by insertion, addition, substitution or deletion of 1 amino acid, 2, 3, 4, 5-10, 10-20 20-30, 30-50, or more than 50 amino acids.

A DA1, DA2 or EOD1 nucleic acid in a plant species of interest may have a nucleotide sequence which is a variant of a respective DA1, DA2 or EOD1 reference nucleotide sequence set out herein. For example, variant nucleotide sequence may be a homologue, or allele of a reference DA1, DA2 or EOD1 sequence set out herein, and may differ from the reference DA1, DA2 or EOD1 nucleotide sequence by one or more of addition, insertion, deletion or substitution of one or more nucleotides in the nucleic acid, for example 2, 3, 4, 5-10, 10-20 20-30, 30-50, or more than 50, leading to the addition, insertion, deletion or substitution of one or more amino acids in the encoded polypeptide. Of course, changes to the nucleic acid that make no difference to the encoded amino acid sequence are included. A DA1, DA2 or EOD1 encoding nucleic acid may comprise a sequence having at least 20% or at least 30% sequence identity with the reference nucleic acid sequence, preferably at least 40%, at least 50%, at least 60%, at least 65%, at least 70%, at least 80%, at least 90%, at least 95% or at least 98%. Sequence identity is described above.

Sequence similarity and identity are commonly defined with reference to the algorithm GAP (Wisconsin Package, Accelerys, San Diego USA). GAP uses the Needleman and Wunsch algorithm to align two complete sequences that maximizes the number of matches and minimizes the number of gaps. Generally, default parameters are used, with a gap creation penalty=12 and gap extension penalty=4. Use of GAP may be preferred but other algorithms may be used, e.g. BLAST (which uses the method of Altschul et al. (1990) J. Mol. Biol. 215: 405-410), FASTA (which uses the method of Pearson and Lipman (1988) PNAS USA 85: 2444-2448), or the Smith-Waterman algorithm (Smith and Waterman (1981) J. Mol Biol. 147: 195-197), or the TBLASTN program, of Altschul et al. (1990) supra, generally employing default parameters. In particular, the psi-Blast algorithm (Nucl. Acids Res. (1997) 25 3389-3402) may be used.

Sequence comparison may be made over the full-length of the relevant sequence described herein.

Suitable variant amino acid and nucleotide sequences can be identified in any plant species of interest using standard sequence analysis techniques.

A DA1, DA2 or EOD1 nucleotide sequence which is a variant of a reference DA1, DA2 or EOD1 nucleic acid sequence set out herein, may selectively hybridise under stringent conditions with this nucleic acid sequence or the complement thereof.

Stringent conditions include, e.g. for hybridization of sequences that are about 80-90% identical, hybridization overnight at 42° C. in 0.25M Na₂HPO₄, pH 7.2, 6.5% SDS, 10% dextran sulfate and a final wash at 55° C. in 0.1×SSC, 0.1% SDS. For detection of sequences that are greater than about 90% identical, suitable conditions include hybridization overnight at 65° C. in 0.25M Na₂HPO₄, pH 7.2, 6.5% SDS, 10% dextran sulfate and a final wash at 60° C. in 0.1×SSC, 0.1% SDS.

An alternative, which may be particularly appropriate with plant nucleic acid preparations, is a solution of 5×SSPE (final 0.9 M NaCl, 0.05M sodium phosphate, 0.005M EDTA pH 7.7), 5X Denhardt's solution, 0.5% SDS, at 50° C. or 65° C. overnight. Washes may be performed in 0.2×SSC/0.1% SDS at 65° C. or at 50-60° C. in 1×SSC/0.1% SDS, as required.

Nucleic acids as described herein may be wholly or partially synthetic. In particular, they may be recombinant in that nucleic acid sequences which are not found together in nature (do not run contiguously) have been ligated or otherwise combined artificially. Alternatively, they may have been synthesised directly e.g. using an automated synthesiser.

The expression of a DA2 nucleic acid and a DA1 and/or EOD1 nucleic acid may reduced or abolished in one or more cells of a plant by any convenient technique.

Methods for reducing the expression or activity of a DA2 polypeptide and a DA1 and/or EOD1 polypeptide in a plant are well-known in the art and are described in more detail below. In some embodiments, the expression of active DA2, DA1 and/or EOD1 polypeptide may be reduced, preferably abolished, by introducing a mutation into the nucleic acid sequence in a plant cell which encodes the polypeptide or which regulate the expression of such a nucleic acid sequence. The mutation may disrupt the expression or function of the DA2, DA1 and/or EOD1 polypeptide. Suitable mutations include knock-out and knock-down mutations. In some embodiments, a mutation may produce a dominant-negative allele of DA1. A plant may then be regenerated from the mutated cell. The nucleic acids may be mutated by insertion or deletion of one or more nucleotides. Techniques for the mutagenesis, inactivation or knockout of target genes are well-known in the art (see for example In Vitro Mutagenesis Protocols; Methods in Molecular Biology (2nd edition) Ed Jeff Braman; Sambrook J et al. 2012. Molecular Cloning: A Laboratory Manual (4th Edition) CSH Press; Current Protocols in Molecular Biology; Ed Ausubel et al (2013) Wiley). In some embodiments, mutations may be introduced into a target EOD1, DA2 or DA1 gene by genome editing techniques, for example RNA guided nuclease techniques such as CRISPR, Zinc-finger nucleases (ZFNs) and transactivator-like effector nucleases (TALENs) (Urnov, F. D. et al Nature reviews. Genetics 11, 636-646 (2010); Joung, J. K. et al. Nature reviews. Molecular cell biology 14, 49-55 (2013); Gasiunas, G. et al PNAS USA 109, E2579-2586 (2012); Cong, L. et al. Science 339, 819-823 (2013)).

Sequence mutations which reduce the expression or activity may include a deletion, insertion or substitution of one or more nucleotides, relative to the wild-type nucleotide sequence, a gene amplification or an increase or decrease in methylation, for example hypermethylation. The one or more mutations may be in a coding or non-coding region of the nucleic acid sequence. Mutations in the coding region of the gene encoding the component may prevent the translation of full-length active protein i.e. truncating mutations, or allow the translation of full-length but inactive or impaired function protein i.e. mis-sense mutations. Mutations or epigenetic changes, such as methylation, in non-coding regions of the gene encoding the component, for example, in a regulatory element, may prevent transcription of the gene. A nucleic acid comprising one or more sequence mutations may encode a variant polypeptide which has reduced or abolished activity or may encode a wild-type polypeptide which has little or no expression within the cell, for example through the altered activity of a regulatory element. A nucleic acid comprising one or more sequence mutations may have one, two, three, four or more mutations relative to the unmutated sequence.

For example, the activity of EOD1 may be reduced, preferably abolished, by introducing a mutation, such as a deletion, insertion or substitution, at a position corresponding to position 44 of SEQ ID NO: 89, for example, an A to T substitution. A position in a EOD1 polypeptide sequence which is equivalent to position 44 of SEQ ID NO: 89 may be identified using standard sequence analysis and alignment tools, as shown in Table 4.

DA2, DA1 and EOD1 coding sequences may be identified in any plant species of interest using standard sequence analysis techniques, for example by comparison with the reference sequences set out herein.

Mutations suitable for abolishing expression of an active DA2, DA1 and/or EOD1 polypeptide will be readily apparent to the skilled person.

In some preferred embodiments, a mutation that reduces or abolishes DA2 expression or activity may be introduced into a plant cell that expresses a dominant negative DA1 polypeptide and optionally comprises either i) a heterologous nucleic acid that encodes an EOD1 suppressor nucleic acid or ii) a mutation that reduces EOD1 expression or activity.

In some embodiments, the expression of a DA1, DA2 and/or EOD1 polypeptide may be reduced in a plant cell by expressing a heterologous nucleic acid which encodes or transcribes a suppressor nucleic acid, for example a suppressor RNA or RNAi molecule, within cells of said plant. The suppressor RNA suppresses the expression of its target polypeptide (i.e. DA1, DA2 or EOD1) in the plant cells.

Nucleic acids as described herein may be wholly or partially synthetic. In particular, they may be recombinant in that nucleic acid sequences which are not found together in nature (do not run contiguously) have been ligated or otherwise combined artificially. Alternatively, they may have been synthesised directly e.g. using an automated synthesiser.

The nucleic acid may of course be double- or single-stranded, cDNA or genomic DNA, or RNA. The nucleic acid may be wholly or partially synthetic, depending on design. Naturally, the skilled person will understand that where the nucleic acid includes RNA, reference to the sequence shown should be construed as reference to the RNA equivalent, with U substituted for T.

“Heterologous” indicates that the gene/sequence of nucleotides in question or a sequence regulating the gene/sequence in question, has been introduced into said cells of the plant or an ancestor thereof, using genetic engineering or recombinant means, i.e. by human intervention. Nucleotide sequences which are heterologous to a plant cell may be non-naturally occurring in cells of that type, variety or species (i.e. exogenous or foreign) or may be sequences which are non-naturally occurring in that sub-cellular or genomic environment of the cells or may be sequences which are non-naturally regulated in the cells i.e. operably linked to a non-natural regulatory element.

The suppression of the expression of a target polypeptide in plant cells is well-known in the art. A suitable suppressor nucleic acid may be a copy of all or part of the target DA1, DA2 and/or EOD1 gene inserted in antisense or sense orientation or both relative to the DA1, DA2 and/or EOD1 gene, to achieve reduction in expression of the target gene. See, for example, van der Krol et al., (1990) The Plant Cell 2, 291-299; Napoli et al., (1990) The Plant Cell 2, 279-289; Zhang et al., (1992) The Plant Cell 4, 1575-1588, and US-A-5,231,020. Further refinements of this approach may be found in WO95/34668 (Biosource); Angell & Baulcombe (1997) The EMBO Journal 16, 12:3675-3684; and Voinnet & Baulcombe (1997) Nature 389: pg 553. In some embodiments, the suppressor nucleic acid may be a sense suppressor of expression of the DA1, DA2 and/or EOD1 polypeptide.

A suitable sense suppressor nucleic acid may be a double stranded RNA (Fire A. et al Nature, Vol 391, (1998)). dsRNA mediated silencing is gene specific and is often termed RNA interference (RNAi). RNAi is a two-step process. First, dsRNA is cleaved within the cell to yield short interfering RNAs (siRNAs) of about 21-23nt length with 5′ terminal phosphate and 3′ short overhangs (-2nt). The siRNAs target the corresponding mRNA sequence specifically for destruction (Zamore P.D. Nature Structural Biology, 8, 9, 746-750, (2001)). siRNAs (sometimes called microRNAs) down-regulate gene expression by binding to complementary RNAs and either triggering mRNA elimination (RNAi) or arresting mRNA translation into protein. siRNA may be derived by processing of long double stranded RNAs and when found in nature are typically of exogenous origin. Micro-interfering RNAs (miRNA) are endogenously encoded small non-coding RNAs, derived by processing of short hairpins. Both siRNA and miRNA can inhibit the translation of mRNAs bearing partially complementary target sequences without RNA cleavage and degrade mRNAs bearing fully complementary sequences.

Accordingly, the present invention provides the use of RNAi sequences based on the DA1, DA2 and/or EOD1 nucleic acid sequence for suppression of the expression of the DA1, DA2 and/or EOD1 polypeptide. For example, an RNAi sequence may correspond to a fragment of a reference DA2, DA1 or EOD1 nucleotide sequence set out herein or may be a variant thereof.

siRNA molecules are typically double stranded and, in order to optimise the effectiveness of RNA mediated down-regulation of the function of a target gene, it is preferred that the length and sequence of the siRNA molecule is chosen to ensure correct recognition of the siRNA by the RISC complex that mediates the recognition by the siRNA of the mRNA target and so that the siRNA is short enough to reduce a host response.

miRNA ligands are typically single stranded and have regions that are partially complementary enabling the ligands to form a hairpin. miRNAs are RNA sequences which are transcribed from DNA, but are not translated into protein. A DNA sequence that codes for a miRNA is longer than the miRNA. This DNA sequence includes the miRNA sequence and an approximate reverse complement. When this DNA sequence is transcribed into a single-stranded RNA molecule, the miRNA sequence and its reverse-complement base pair to form a partially double stranded RNA segment. The design of microRNA sequences is discussed on John et al, PLoS Biology, 11(2), 1862-1879, 2004.

Typically, the RNA molecules intended to mimic the effects of siRNA or miRNA have between 10 and 40 ribonucleotides (or synthetic analogues thereof), more preferably between 17 and 30 ribonucleotides, more preferably between 19 and 25 ribonucleotides and most preferably between 21 and 23 ribonucleotides. In some embodiments of the invention employing double-stranded siRNA, the molecule may have symmetric 3′ overhangs, e.g. of one or two (ribo)nucleotides, typically a UU of dTdT 3′ overhang. Based on the disclosure provided herein, the skilled person can readily design suitable siRNA and miRNA sequences, for example using resources such as siRNA finder (Ambion). siRNA and miRNA sequences can be synthetically produced and added exogenously to cause gene downregulation or produced using expression systems (e.g. vectors). In a preferred embodiment, the siRNA is synthesized synthetically.

Longer double stranded RNAs may be processed in the cell to produce siRNAs (see for example Myers (2003) Nature Biotechnology 21:324-328). The longer dsRNA molecule may have symmetric 3′ or 5′ overhangs, e.g. of one or two (ribo) nucleotides, or may have blunt ends. The longer dsRNA molecules may be 25 nucleotides or longer. Preferably, the longer dsRNA molecules are between 25 and 30 nucleotides long. More preferably, the longer dsRNA molecules are between 25 and 27 nucleotides long. Most preferably, the longer dsRNA molecules are 27 nucleotides in length. dsRNAs 30 nucleotides or more in length may be expressed using the vector pDECAP (Shinagawa et al., Genes and Dev., 17, 1340-5, 2003).

Another alternative is the expression of a short hairpin RNA molecule (shRNA) in the cell. shRNAs are more stable than synthetic siRNAs. A shRNA consists of short inverted repeats separated by a small loop sequence. One inverted repeat is complementary to the gene target. In the cell the shRNA is processed by DICER into a siRNA which degrades the target gene mRNA and suppresses expression. In a preferred embodiment the shRNA is produced endogenously (within a cell) by transcription from a vector. shRNAs may be produced within a cell by transfecting the cell with a vector encoding the shRNA sequence under control of a RNA polymerase III promoter such as the human H1 or 7SK promoter or a RNA polymerase II promoter. Alternatively, the shRNA may be synthesised exogenously (in vitro) by transcription from a vector. The shRNA may then be introduced directly into the cell. Preferably, the shRNA molecule comprises a partial sequence of DA1, DA2 and/or EOD1. For example, the shRNA sequence is between 40 and 100 bases in length, more preferably between 40 and 70 bases in length. The stem of the hairpin is preferably between 19 and 30 base pairs in length. The stem may contain G-U pairings to stabilise the hairpin structure.

siRNA molecules, longer dsRNA molecules or miRNA molecules may be made recombinantly by transcription of a nucleic acid sequence, preferably contained within a vector. Preferably, the siRNA molecule, longer dsRNA molecule or miRNA molecule comprises a partial sequence of a reference DA2, DA1 or EOD1 nucleotide sequence set out herein or a variant thereof.

In other embodiments, the suppressor nucleic acid may be an anti-sense suppressor of expression of the DA1, DA2 and/or EOD1 polypeptide. In using anti-sense sequences to down-regulate gene expression, a nucleotide sequence is placed under the control of a promoter in a “reverse orientation” such that transcription yields RNA which is complementary to normal mRNA transcribed from the “sense” strand of the target gene. See, for example, Rothstein et al, 1987; Smith et a/,(1988) Nature 334, 724-726; Zhang et a/,(1992) The Plant Cell 4, 1575-1588, English et al., (1996) The Plant Cell 8, 179-188. Antisense technology is also reviewed in Bourque, (1995), Plant Science 105, 125-149, and Flavell (1994) PNAS USA 91, 3490-3496.

An anti-sense suppressor nucleic acid may comprise an anti-sense sequence of at least 10 nucleotides from a nucleotide sequence is a fragment of a reference DA2, DA1 or EOD1 nucleotide sequence set out herein or a variant thereof.

It may be preferable that there is complete sequence identity in the sequence used for down-regulation of expression of a target sequence, and the target sequence, although total complementarity or similarity of sequence is not essential. One or more nucleotides may differ in the sequence used from the target gene. Thus, a sequence employed in a down-regulation of gene expression in accordance with the present invention may be a wild-type sequence (e.g. gene) selected from those available, or a variant of such a sequence.

The sequence need not include an open reading frame or specify an RNA that would be translatable. It may be preferred for there to be sufficient homology for the respective anti-sense and sense RNA molecules to hybridise. There may be down regulation of gene expression even where there is about 5%, 10%, 15% or 20% or more mis-match between the sequence used and the target gene. Effectively, the homology should be sufficient for the down-regulation of gene expression to take place.

A suppressor RNA molecule may comprise 10-40 nucleotides of the sense or anti-sense strand of a nucleic acid sequence which encodes DA2, DA1 and/or EOD1 polypeptide.

Suppressor nucleic acids may be operably linked to heterologous promoters, for example tissue-specific or inducible promoters. For example, integument and seed specific promoters can be used to specifically down-regulate two or more DA1, DA2 and/or EOD1 nucleic acids in developing ovules and seeds to increase final seed size.

In some preferred embodiments, DA2 suppressor nucleic acid may be expressed in a plant cell with a nucleic acid encoding a dominant negative DA1 polypeptide and optionally an EOD1 suppressor nucleic acid.

Nucleic acid encoding the suppressor nucleic acid and/or a dominant-negative DA1 polypeptide may be comprised in one or more vectors.

Nucleic acid encoding the suppressor nucleic acid(s) as described herein and/or dominant-negative DA1 polypeptide may be operably linked to a heterologous regulatory sequence, such as a promoter, for example a constitutive, inducible, tissue-specific or developmental specific promoter as described above.

Nucleic acid encoding suppressor nucleic acid(s) as described herein and/or dominant negative DA1 polypeptides may be contained on a nucleic acid construct or vector. The construct or vector is preferably suitable for transformation into and/or expression within a plant cell. A vector is, inter alia, any plasmid, cosmid, phage or Agrobacterium binary vector in double or single stranded linear or circular form, which may or may not be self-transmissible or mobilizable, and which can transform prokaryotic or eukaryotic host, in particular a plant host, either by integration into the cellular genome or exist extrachromasomally (e.g. autonomous replicating plasmid with an origin of replication).

Specifically included are shuttle vectors by which is meant a DNA vehicle capable, naturally or by design, of replication in two different organisms, which may be selected from Actinomyces and related species, bacteria and eukaryotic (e.g. higher plant, mammalia, yeast or fungal) cells.

A construct or vector comprising nucleic acid as described above need not include a promoter or other regulatory sequence, particularly if the vector is to be used to introduce the nucleic acid into cells for recombination into the genome.

Constructs and vectors may further comprise selectable genetic markers consisting of genes that confer selectable phenotypes such as resistance to antibiotics such as kanamycin, hygromycin, phosphinotricin, chlorsulfuron, methotrexate, gentamycin, spectinomycin, imidazolinones, glypho sate and d-amino acids.

Those skilled in the art can construct vectors and design protocols for recombinant gene expression, for example in a microbial or plant cell. Suitable vectors can be chosen or constructed, containing appropriate regulatory sequences, including promoter sequences, terminator fragments, polyadenylation sequences, enhancer sequences, marker genes and other sequences as appropriate. For further details see, for example, Molecular Cloning: a Laboratory Manual: 3rd edition, Sambrook et al, 2001, Cold Spring Harbor Laboratory Press and Protocols in Molecular Biology, Second Edition, Ausubel et al. eds. John Wiley & Sons, 1992. Specific procedures and vectors previously used with wide success upon plants are described by Bevan, Nucl. Acids Res. (1984) 12, 8711-8721), and Guerineau and Mullineaux, (1993) Plant transformation and expression vectors. In: Plant Molecular Biology Labfax (Croy RRD ed) Oxford, BIOS Scientific Publishers, pp 121-148.

When introducing a chosen gene construct into a cell, certain considerations must be taken into account, well known to those skilled in the art. The nucleic acid to be inserted should be assembled within a construct that contains effective regulatory elements that will drive transcription. There must be available a method of transporting the construct into the cell. Once the construct is within the cell membrane, integration into the endogenous chromosomal material either will or will not occur. Finally, the target cell type is preferably such that cells can be regenerated into whole plants.

It is desirable to use a construct and transformation method which enhances expression of the nucleic acid encoding the suppressor nucleic acid or dominant negative DA1 polypeptide. Integration of a single copy of the gene into the genome of the plant cell may be beneficial to minimize gene silencing effects. Likewise, control of the complexity of integration may be beneficial in this regard. Of particular interest in this regard is transformation of plant cells utilizing a minimal gene expression construct according to, for example, EP Patent No. EP1407000B1, herein incorporated by reference for this purpose.

Techniques well known to those skilled in the art may be used to introduce nucleic acid constructs and vectors into plant cells to produce transgenic plants with the properties described herein.

Agrobacterium transformation is one method widely used by those skilled in the art to transform plant species. Production of stable, fertile transgenic plants is now routine in the art(see for example Toriyama, et al. (1988) Bio/Technology 6, 1072-1074; Zhang, et al. (1988) Plant Cell Rep. 7, 379-384; Zhang, et al. (1988) Theor Appl Genet 76, 835-840; Shimamoto, et al. (1989) Nature 338, 274-276; Datta, et al. (1990) Bio/Technology 8, 736-740; Christou, et al. (1991) Bio/Technology 9, 957-962; Peng, et al. (1991) International Rice Research Institute, Manila, Philippines 563-574; Cao, et al. (1992) Plant Cell Rep. 11, 585-591; Li, et al. (1993) Plant Cell Rep. 12, 250-255; Rathore, et al. (1993) Plant Molecular Biology 21, 871-884; Fromm, et al. (1990) Bio/Technology 8, 833-839; Gordon-Kamm, et al. (1990) Plant Cell 2, 603-618; D′Halluin, et al. (1992) Plant Cell 4, 1495-1505; Walters, et al. (1992) Plant Molecular Biology 18, 189-200; Koziel, et al. (1993) Biotechnology 11, 194-200; Vasil, I. K. (1994) Plant Molecular Biology 25, 925-937; Weeks, et al. (1993) Plant Physiology 102, 1077-1084; Somers, et al. (1992) Bio/Technology 10, 1589-1594; WO92/14828; Nilsson, O. et al (1992) Transgenic Research 1, 209-220).

Other methods, such as microprojectile or particle bombardment (US 5100792, EP-A-444882, EP-A-434616), electroporation (EP 290395, WO 8706614), microinjection (WO 92/09696, WO 94/00583, EP 331083, EP 175966, Green et al. (1987) Plant Tissue and Cell Culture, Academic Press), direct DNA uptake (DE 4005152, WO 9012096, US 4684611), liposome mediated DNA uptake (e.g. Freeman et al. Plant Cell Physiol. 29: 1353 (1984)) or the vortexing method (e.g. Kindle, PNAS U.S.A. 87: 1228 (1990d)) may be preferred where Agrobacterium transformation is inefficient or ineffective, for example in some gymnosperm species. Physical methods for the transformation of plant cells are reviewed in Oard, 1991, Biotech. Adv. 9: 1-11.

Alternatively, a combination of different techniques may be employed to enhance the efficiency of the transformation process, e.g. bombardment with Agrobacterium coated microparticles (EP-A-486234) or microprojectile bombardment to induce wounding followed by co-cultivation with Agrobacterium (EP-A-486233).

Following transformation, a plant may be regenerated, e.g. from single cells, callus tissue or leaf discs, as is standard in the art. Almost any plant can be entirely regenerated from cells, tissues and organs of the plant. Available techniques are reviewed in Vasil et al., Cell Culture and Somatic Cell Genetics of Plants, Vol I, II and III, Laboratory Procedures and Their Applications, Academic Press, 1984, and Weissbach and Weissbach, Methods for Plant Molecular Biology, Academic Press, 1989.

The particular choice of a transformation technology will be determined by its efficiency to transform certain plant species as well as the experience and preference of the person practising the invention with a particular methodology of choice. It will be apparent to the skilled person that the particular choice of a transformation system to introduce nucleic acid into plant cells is not essential to or a limitation of the invention, nor is the choice of technique for plant regeneration.

Following transformation, a plant cell with reduced DA2 expression and reduced DA1 and/or EOD1 expression or activity may be identified and/or selected. A plant may be regenerated from the plant cell.

A plant with reduced DA2 activity or expression that is also deficient in the expression or activity of DA1, EOD1 or both DA1 and EOD1, as described above may be sexually or asexually propagated or grown to produce off-spring or descendants. Off-spring or descendants of the plant regenerated from the one or more cells may be sexually or asexually propagated or grown. The plant or its off-spring or descendents may be crossed with other plants or with itself.

The DA1, DA2 and/or EOD1 amino acid or nucleic acid sequence may be employed as a molecular marker to determine the expression or activity of one or more of the DA1, DA2 and/or EOD1 polypeptides in a plant before, during or after growing or sexually or asexually propagated as set out above. A method may comprise:

-   -   providing a population of plants,

determining the amount of expression of an DA1, DA2 and/or EOD1 polypeptide in one or more plants in the population, and

-   -   identifying one or more plants in the population with reduced         expression of the DA1, DA2 and/or EOD1 polypeptide relative to         other members of said population.

The population of plants may be produced as described above.

In some embodiments, a method may comprise:

crossing a first and a second plant to produce a population of progeny plants;

determining the expression of one or more of DA1, DA2 and EOD1 polypeptides in the progeny plants in the population, and

identifying a progeny plant in the population in which expression of the DA1, DA2 and/or EOD1 polypeptide is reduced relative to controls.

One or both of the first and second plants may be produced as described above.

A progeny plant in which expression of the DA2 and DA1 and/or EOD1 polypeptide is reduced relative to controls (e.g. other members of the population) may display increased seed and/or organ size relative to the controls and may have higher plant yields.

In some embodiments, DA1 and EOD1 amino acid or nucleic acid sequences may be employed as a molecular marker to determine the expression or activity of one or more of the DA1 and/or EOD1 polypeptides in a plant in order to identify a plant or plant cell deficient in DA1 and/or EOD1 in which expression or activity of a DA2 polypeptide may be reduced as described above. A method may comprise:

-   -   providing a population of plants,     -   determining the amount of expression of an DA1 and/or EOD1         polypeptide in one or more plants in the population, and     -   identifying one or more plants in the population with reduced         expression of the DA1 and/or EOD1 polypeptide relative to other         members of said population.

DA2 expression or activity may be reduced in the identified plants as methods described above.

A plant or progeny plant may be identified by i) measuring the amount of DA1, DA2 and/or EOD1 polypeptide in one or more cells of the plant ii) measuring the amount of DA1, DA2 and/or EOD1 mRNA in one or more cells of the plant or iii) sequencing the nucleic acid encoding the DA1, DA2 and/or EOD1 polypeptide in one or more cells of the plant and identifying the presence of one or more mutations.

The identified plants may be further propagated or crossed, for example, with other plants having reduced DA1, DA2 and/or EOD1 expression or self-crossed to produce inbred lines. The expression or activity of a DA1, DA2 and/or EOD1 polypeptide in populations of progeny plants may be determined and one or more progeny plants with reduced expression or activity of DA1, DA2 and/or EOD1 identified.

In some embodiments, the amount of expression of DA1, DA2 and/or EOD1 may be determined at the protein level. A method may comprise:

providing a population of plants,

determining the amount of DA1, DA2 and/or EOD1 polypeptide in one or more plants of said population, and

identifying one or more plants in the population with reduced amount of an DA1, DA2 and/or EOD1 polypeptide relative to other members of said population.

Conveniently, immunological techniques, such as Western blotting, may be employed, using antibodies which bind to the DA1, DA2 or EOD1 polypeptide and show little or no binding to other antigens in the plant. For example, the amount of an DA1, DA2 and/or EOD1 polypeptide in a plant cell may be determined by contacting a sample comprising the plant cell with an antibody or other specific binding member directed against the DA1, DA2 or EOD1 polypeptide, and determining binding of the DA1, DA2 or EOD1 polypeptide to the sample. The amount of binding of the specific binding member is indicative of the amount of DA1, DA2 or EOD1 polypeptide which is expressed in the cell.

The amount of DA1, DA2 and/or EOD1 polypeptide may be determined in one or more cells of the plant, preferably cells from an above-ground portion or tissue of the plant, such as the vasculature and primary and secondary meristems in the shoot.

In other embodiments, the expression of the DA1, DA2 or EOD1 polypeptide may be determined at the nucleic acid level. For example, the amount of nucleic acid encoding a DA1, DA2 or EOD1 polypeptide may be determined. A method of producing a plant having increased yield related traits may comprise:

providing a population of plants,

determining the level or amount of nucleic acid, for example mRNA, encoding the DA1, DA2 or EOD1 polypeptide in a cell of one or more plants of said population, and,

identifying one or more plants in the population with reduced amount of an DA1, DA2 or EOD1 encoding nucleic acid relative to other members of said population.

The level or amount of encoding nucleic acid in a plant cell may be determined for example by detecting the amount of transcribed encoding nucleic acid in the cell. This may be performed using standard techniques such as Northern blotting or RT-PCR.

Alternatively, the presence of sequence variations which affect the expression or activity of a DA1, DA2 or EOD1 polypeptide may be determined. Another method of producing a plant having increased growth and/or biomass may comprise:

providing a population of plants,

determining the presence of one or more sequence variations, for example, polymorphisms, mutations or regions of hypermethylation, in a nucleic acid encoding an DA1, DA2 and/or EOD1 polypeptide in a cell in one or more plants of said population,

wherein said one or more sequence variations which reduce the expression or activity of the encoded DA1, DA2 and/or EOD1 polypeptide, and

identifying one or more plants in the population with one or more sequence variations which reduce the expression or activity of DA1, DA2 and/or EOD1 relative to other members of said population.

DA1, DA2 and/or EOD1 polypeptides and encoding nucleic acid are described in more detail above.

The presence of one or more sequence variations in a nucleic acid may be determined by detecting the presence of the variant nucleic acid sequence in one or more plant cells or by detecting the presence of the variant polypeptide which is encoded by the nucleic acid sequence. Preferred nucleic acid sequence variation detection techniques include ARMS™-allele specific amplification, OLA, ALEX™, COPS, Taqman, Molecular Beacons, RFLP, and restriction site based PCR and FRET techniques.

Numerous suitable methods for determining the amount of a nucleic acid encoding an DA1, DA2 or EOD1 polypeptide, or the presence or absence of sequence variation in a nucleic acid encoding an DA1, DA2 or EOD1 polypeptide, in a plant cell, are available in the art (see for example (see for example Molecular Cloning: a Laboratory Manual: 3rd edition, Sambrook & Russell (2001) Cold Spring Harbor Laboratory Press NY; Current Protocols in Molecular Biology, Ausubel et al. eds. John Wiley & Sons (1992); DNA Cloning, The Practical Approach Series (1995), series eds. D. Rickwood and B.D. Hames, IRL Press, Oxford, UK and PCR Protocols: A Guide to Methods and Applications (Innis, et al. 1990. Academic Press, San Diego, Calif.)). Many current methods for the detection of sequence variation are reviewed by Nollau et al., Clin. Chem. 43, 1114-1120, 1997; and in standard textbooks, for example “Laboratory Protocols for Mutation Detection”, Ed. by U. Landegren, Oxford University Press, 1996 and “PCR”, 2^(nd) Edition by Newton & Graham, BIOS Scientific Publishers Limited, 1997.

Preferred polypeptide sequence variation techniques include immunoassays, which are well known in the art e.g. A Practical Guide to ELISA by D M Kemeny, Pergamon Press 1991; Principles and Practice of Immunoassay, 2^(nd) edition, C P Price & D J Newman, 1997, published by Stockton Press in USA & Canada and by Macmillan Reference in the United Kingdom.

In some embodiments, nucleic acid or an amplified region thereof may be sequenced to identify or determine the presence of polymorphism or mutation therein. A polymorphism or mutation may be identified by comparing the sequence obtained with the known sequence of DA1, DA2 or EOD1, for example as set out in sequence databases. Alternatively, it can be compared to the sequence of the corresponding nucleic acid from control cells. In particular, the presence of one or more polymorphisms or mutations that cause reduction but not total abrogation of function may be determined. Sequencing may be performed using any one of a range of standard techniques. Sequencing of an amplified product may, for example, involve precipitation with isopropanol, resuspension and sequencing using a TaqFS+ Dye terminator sequencing kit (e.g. from GE Healthcare UK Ltd UK). Extension products may be electrophoresed on an ABI 377 DNA sequencer and data analysed using Sequence Navigator software.

A progeny plant identified as having reduced DA1, DA2 and/or EOD1 expression may be tested for increased or enhanced yield related traits, such as increased seed or organ size, relative to controls.

The identified progeny plant may be further propagated or crossed, for example with the first or second plant (i.e. backcrossing) or self-crossed to produce inbred lines.

The identified progeny plant may be tested for seed size, organ size and/or plant yield relative to controls.

A plant produced as described herein may be deficient in DA2 expression or activity and may be further deficient in DA1 expression or activity, EOD1 expression or activity or both DA1 and EOD1 expression or activity.

The expression or activity of DA2, DA1 and EOD1 may be reduced or abolished in the plant by mutation or one or more nucleotides in the plant coding sequence and/or by the expression of a heterologous nucleic acid encoding a suppressor nucleic acid. In some preferred embodiments, the activity of DA1 may be reduced or abolished in the plant by expression of a heterologous nucleic acid encoding a dominant-negative DA1 polypeptide.

A plant may thus comprise heterologous nucleic acid which encodes a suppressor nucleic acid, such as an siRNA or shRNA, which reduces the expression of one or more of DA1, DA2 and EOD1 or which encodes a dominant negative DA1 polypeptide.

Any combination of mutations, suppressor nucleic acids may be employed in a plant as described herein. For example, a plant may comprise i) a mutation which reduces DA2 activity or expression, a heterologous nucleic acid encoding a suppressor nucleic acid which reduces EOD1 expression and a heterologous nucleic acid encoding a nucleic acid which encodes a dominant-negative DA1 polypeptide; ii) a heterologous nucleic acid encoding a suppressor nucleic acid which reduces DA2 expression or expression, a mutation which reduces EOD1 expression and a heterologous nucleic acid encoding a nucleic acid which encodes a dominant-negative DA1 polypeptide iii) heterologous nucleic acids encoding suppressor nucleic acids which reduce EOD1 and DA2 expression and a heterologous nucleic acid encoding a nucleic acid which encodes a dominant-negative DA1 polypeptide, or iv) mutation which reduce EOD1 and DA2 activity or expression and a heterologous nucleic acid encoding a nucleic acid which encodes a dominant-negative DA1 polypeptide.

In other embodiments, a plant may comprise i) a mutation which reduces DA2 activity or expression, a heterologous nucleic acid encoding a suppressor nucleic acid which reduces DA1 expression ii) a heterologous nucleic acid encoding a suppressor nucleic acid which reduces DA2 expression or expression, a mutation which reduces DA1 expression iii) heterologous nucleic acids encoding suppressor nucleic acids which reduce DA1 and DA2 expression, iv) mutations which reduce DA1 and DA2 activity or expression or v) a mutation which reduces DA2 activity or expression or a heterologous nucleic acid encoding a suppressor nucleic acid which reduces DA2 expression and a heterologous nucleic acid encoding a nucleic acid which encodes a dominant negative DA1 polypeptide.

Heterologous nucleic acids encoding the dominant-negative DA1 polypeptide and/or suppressor nucleic acids may be on the same or different expression vectors and may be incorporated into the plant cell by conventional techniques.

Examples of suitable plants for use in accordance with any aspect of the invention described herein include monocotyledonous and dicotelydonous higher plant, for example an agricultural or crop plant, such as a plant selected from the group consisting of Lithospermum erythrorhizon, Taxus spp, tobacco, cucurbits, carrot, vegetable brassica, melons, capsicums, grape vines, lettuce, strawberry, oilseed brassica, sugar beet, wheat, barley, maize, rice, soyabeans, peas, sorghum, sunflower, tomato, potato, pepper, chrysanthemum, carnation, linseed, hemp and rye.

A plant produced as described above may be sexually or asexually propagated or grown to produce off-spring or descendants. Off-spring or descendants of the plant regenerated from the one or more cells may be sexually or asexually propagated or grown. The plant or its off-spring or descendents may be crossed with other plants or with itself.

Another aspect of the invention provides a transgenic plant having reduced or abolished expression or activity of DA2 polypeptide within one or more cells thereof, wherein the plant is deficient in the expression or activity of DA1, EOD1 or both DA1 and EOD1.

The plant may comprise an exogenous nucleic acid which reduces or abolishes the expression or activity of one or more of DA2, DA1 and EOD1. In some embodiments, the transgenic plant may express a dominant negative DA1 polypeptide that reduces the activity of DA1.

In some embodiments, the plant may have reduced or abolished expression of DA1, DA2 and EOD1 or may have reduced or abolished expression of DA2 and EOD1 and may express a dominant negative DA1.

In addition to a plant produced by a method described herein, the invention encompasses any clone of such a plant, seed, selfed or hybrid progeny and descendants, and any part or propagule of any of these, such as cuttings and seed, which may be used in reproduction or propagation, sexual or asexual. Also encompassed by the invention is a plant which is a sexually or asexually propagated off-spring, clone or descendant of such a plant, or any part or propagule of said plant, off-spring, clone or descendant.

A suitable plant may be produced by a method described above.

The plant may have increased yield relative to control wild-type plants (i.e. identical plants in which the expression or activity of DA2 and optionally DA1 and/or EOD1 has not been reduced). For example, the mass of seeds (e.g. grain) or other plant product per unit area may be increased relative to control plants.

For example, one or more yield-related traits in the plant may be improved. Yield-related traits may include life-span, organ size and seed size.

A yield related trait may be improved, increased or enhanced in the plant relative to control plants in which expression of the nucleic acid encoding the DA2 polypeptide is not abolished or reduced (i.e. identical plants in which the expression of DA2 and optionally DA1 and/or EOD1 has not been reduced or abolished).

A plant according to the present invention may be one which does not breed true in one or more properties. Plant varieties may be excluded, particularly registrable plant varieties according to Plant Breeders Rights.

DA1 is shown herein to physically interact with DA2 in vivo. Compounds that disrupt or interfere with the interaction may be useful in increasing seed or organ size and improving plant yield.

A method of identifying a compound that increase plant yield may comprise;

determining the effect of a test compound on the binding of a DA2 polypeptide to a DA1 polypeptide,

a reduction or abolition of binding being indicative that the compound may be useful in increasing plant yield.

DA1 and DA2 polypeptides are described in more detail above.

The DA1 and DA2 polypeptides may be isolated or may be expressed recombinant or endogenously in a plant cell.

A compound that reduces or abolises DA1/DA2 binding may be useful in the treatment of plants to increase yield.

“and/or” where used herein is to be taken as specific disclosure of each of the two specified features or components with or without the other. For example “A and/or B” is to be taken as specific disclosure of each of (i) A, (ii) B and (iii) A and B, just as if each is set out individually herein.

Unless context dictates otherwise, the descriptions and definitions of the features set out above are not limited to any particular aspect or embodiment of the invention and apply equally to all aspects and embodiments which are described.

Other aspects and embodiments of the invention provide the aspects and embodiments described above with the term “comprising” replaced by the term “consisting of” and the aspects and embodiments described above with the term “comprising” replaced by the term “consisting essentially of”.

All documents mentioned in this specification are incorporated herein by reference in their entirety for all purposes.

The contents of all database entries mentioned in this specification are also incorporated herein by reference in their entirety for all purposes. This includes the versions of any sequences which are current at the filing date of this application.

EXPERIMENTS 1. Methods 1.1 Plant Materials and Growth Conditions

Arabidopsis ecotype Columbia (Col-0) was the wild type line used. All mutants were in the Col-0 background. da2-1 (SALK_150003) was obtained from Arabidopsis Stock Centre NASC and ABRC collections. The T-DNA insertion was confirmed by PCR and sequencing. Seeds were surface-sterilized with 100% isopropanol for 1 min and 10% (v/v) household bleach for 10min, washed at least three times with sterile water, stratified at 4° C. for 3d in the dark, dispersed on GM medium with 0.9%agar and 1% glucose, and then grown at 22° C. Plants were grown under long-day condition (16h light/8h dark) at 22° C.

1.2 Constructs and Transformation

The pDA2:DA2 construct was made by using a PCR-basedGateway system. The 1960bp promoter sequence of DA2 was amplified using the primers DA2proGW-F and DA2proGW-R. PCR products were then cloned to the pCR8/GW/TOPO TA cloning vector (Invitrogen). The DA2 CDS was amplified and the PCR products were then cloned to the AscI and KpnI sites of the Gateway vector pMDC110 to get the DA2CDS-pMDC110 plasmid. The DA2 promoter was then subcloned to the DA2CDS-pMDC110 by LR reaction to generate the pDA2:DA2 construct. The plasmid pDA2:DA2 was introduced into the da2-1 mutant plants using Agrobacterium tumefaciens GV3101 and transformants were selected on hygromycin (30m/m1) containing medium.

The 35S:DA2 construct was made using a PCR-based Gateway system. PCR products were subcloned into the pCR8/GW/TOPO TA cloning vector (invitrogen) using TOPO enzyme. The DA2 gene was then subcloned into Gateway Binary Vector pMDC32 containing the 35S promoter (Curtis and Grossniklaus, 2003). The plasmid 35S:DA2 was introduced into Col-0 plants using Agrobacterium tumefaciens GV3101 and transformants were selected on hygromycin (30μg/ml) -containing medium.

The 1960 bp promoter sequence of DA2 was amplified and the PCR products were cloned to the pGEM-T vector (Promaga) using T4 DNA ligase and sequenced. The DA2 promoter was then inserted into the Sad and Ncol sites of the binary vector pGreen-GUS (Curtis and Grossniklaus, 2003) to generate the transformation plasmid pDA2: GUS. The plasmid pDA2: GUS was introduced into Col-0 plants using Agrobacterium tumefaciens GV3101 and transformants were selected on kanamycin (50μg/ml) -containing medium. The 35S: GW2 construct was made using a PCR-based Gateway system. PCR products were subcloned into the pCR8/GW/TOPO TA cloning vector (invitrogen) using TOPO enzyme. The GW2 gene was then subcloned into Gateway Binary Vector pMDC32 containing the 35S promoter (Curtis and Grossniklaus, 2003). The plasmid 355: GW2 was introduced into Col-0 plants using Agrobacterium tumefaciens GV3101 and transformants were selected on hygromycin (30m/m1)-containing medium.

1.3 Morphological and Cellular Analysis

Average seed weight was determined by weighing mature dry seeds in batches of 500 using an electronic analytical balance (METTLER MOLEDO AL104 CHINA). The weights of five sample batches were measured for each seed lot. Seeds were photographed under a Leica microscope (LEICA S8APO) using a Leica CCD (DFC420) and seed size were measured by using Image J software. Area measurements of petals (stage 14), leaves, and cotyledons were made by scanning organs to produce a digital image, and then calculating area, length and width by using Image J software. Leaf, petal and embryo cell sizes were measured from DIC images. Biomass accumulation in flowers (stage 14) was measured by weighing organs.

1.4 GUS Staining

Samples (pDA2: GUS) were stained in a solution of 1 mM X-gluc, 100 mM Na3PO4 buffer, 3mM each K3Fe(CN)6/K4Fe(CN)6, 10mM EDTA, and 0.1% Nodidet-P40, and incubated at room temperature for 6 hours. After GUS staining chlorophyll was removed using 70% ethanol.

1.5 RNA Isolation, RT-PCR, and Quantitative Real-Time RT-PCR Analysis

Total RNA was extracted from Arabidopsis roots, stems, leaves, seedlings and inflorescences using an RNeasy Plant Mini kit (TIANGEN, China). Reverse transcription (RT)-PCR was performed as described (Li et al., 2006). cDNA samples were standardized on actin transcript amount using the primers ACTIN2-F and ACTIN2-R. Quantitative real-time RT-PCR analysis was performed with a lightcycler 480 engine (Roche) using the lightcycler 480 SYBR Green Master (Roche). ACTIN7 mRNA was used as an internal control, and relative amounts of mRNA were calculated using the comparative threshold cycle method.

1.6 E3 Ubiquitin Ligase Activity Assay

The coding sequence of DA2 was cloned into BamH I and Pstl sites of the pMAL-C2 vector to generate the construct MBP-DA2. The mutated DA2 (DA2C59S and DA2N91L) were generated by following the instruction manual of multi-site directed mutagenesis kit (Stratagene).

Bacterial lysates expressing MBP-DA2 and mutated MBP-DA2 were prepared from E. coli BL21 induced with 0.4 mM IPTG for 2 hours. Bacteria were lysed in TGH lysis buffer (50 mM HEPES [pH 7.5], 150 mM NaC1, 1.5 mM MgC12, 1 mM EGTA, 1% Triton X-100, 10% glycerol, and protease inhibitor cocktail [Roche]) and sonicated. The lysates were cleared by centrifugation and incubated with amylose resin (New England Biolabs) at 4° Cfor 30 min. Beads were washed by column buffer (20 mM Tris pH7.4, 200 mM NaCl, 1 mM EDTA) and equilibrated by reaction buffer (50 mM Tris pH7.4, 20mM DTT, 5 mM MgC12, 2 mM ATP). 110 ng El (Boston Biochem), 170 ng E2 (Boston Biochem), 1μg His-ubiquitin (Sigma-Aldrich), and 2μg DA2-MBP or mutated DA2-MBP fusion protein was incubated in a 20₁11 reaction buffer for 2 hours at 30° C.

Polyubiquitinated proteins were detected by immunoblotting with an antibody against His (Abmart) and an antibody against MBP (New England Biolabs).

1.7 In Vitro Protein-Protein Interaction

The coding sequences of DA1, da1-1, and DA1 derivatives containing specific protein domains were cloned into BamH I and Not I sites of the pGEX-4T-1 vector to generated GST-DA1, GST-DA1R358K, GST-DA1-UIM, and GST-DA1-LIM+C constructs, and EcoRI and Xhol sites of the pGEX-4T-1 vector to generate GST-DA1-LIM and GST-DA1 -C constructs.

To test protein-protein interaction, bacterial lysates containing approximately 15 μg of MBP-DA2 fusion proteins were combined with lysates containing approximately 30 μg of GST-DA1, GST-DA1R358K, GST-DA1-UIM, GST-DA1-LIM, GST-DA1-LIM+C or GST-DA1-C fusion proteins. 20 μl amylose resin (New England Biolabs) was added into each combined solution with continued rocking at 4° C. for 1 hour. Beads were washed times with TGH buffer, and the isolated proteins were separated on a 10€7c SDS-polyacryamide gel and detected by western blot analysis with anti-GST (Abmart) and anti-MBP antibodies (Abmart), respectively.

1.8 Co-Immunoprecipitation

The coding sequence of DA1 and DA1 -C was cloned into KpnI and BamHI sites of the pCAMBIA1300-221-Myc vector to generate the transformation plasmid 35S::Myc-DA1 and 35S::Myc-DA1-C. PCR products were subcloned into the pCR8/GW/TOPO TA cloning vector (invitrogen) using TOPO enzyme. The DA2 gene was then subcloned into Gateway Binary Vector pMDC43 containing the 35S promoter and the GFP gene (Curtis and Grossniklaus, 2003). PCR products were subcloned into the pCR8/GW/TOPO TA cloning vector (invitrogen) using TOPO enzyme. The PEX10 gene were then subcloned into Gateway Binary Vector pH7FWG2 containing the 35S promoter and the GFP gene.

Nicotiana benthamiana leaves were transformed by injection of Agrobacterium tumefaciens GV3101 cells harboring 35S:Myc-DA1 and 35S:GFP-DA2 plasmids as previously described (Voinnet et al., 2003). Total protein was extracted with extraction buffer (50 mM Tris/HCl, pH 7.5, 150 mM NaCl, 20% glycerol, 2% Triton X-100, 1mM EDTA, lxcomplete protease inhibitor cocktail (Roche) and MG132 20ug/m1) and incubated with GFP-Trap-A (Chromotek) for 1 hour at d 4° C. Beads were washed 3 times with wash buffer (50 mM Tris/HCl, pH 7.5, 150 mM NaCl, 0.1% Triton X-100, and 1× complete protease inhibitor cocktail (Roche)). The immunoprecipitates were separated in 10% SDS-polyacryamide gel and detected by western blot analysis with anti-GFP (Beyotime) and anti-Myc (Abmart) antibodies, respectively.

1.9 Accession Numbers

Arabidopsis Genome Initiative locus identifiers for Arabidopsis genes mentioned herein are as follows: At1g19270 (NP_173361.1 GI: 15221983) (DA1), At4g36860 (NP_195404.6 GI:240256211) (DAR1), At1g78420 (NP_001185425.1 GI:334183988) (DA2), At1g17145 (NP_564016.1 GI:18394446) (DA2L), and At3g63530 (NP_001030922.1 GI: 79316205) (EOD1/BB).

2. Results

2.1 The da2-1 Mutant Produces Large Seeds

To further understand the mechanisms of ubiquitin-mediated control of seed size, we collected the publicly available T-DNA insertion lines of some predicted ubiquitin ligase genes that were expressed in Arabidopsis ovules and/or seeds in several microarray studies and investigated their seed growth phenotypes. From this screen, we identified several T-DNA insertion mutants with altered seed size. We designated one of these mutants da2-1, referring to the order of discovery for large seed size mutants (DA means “large” in Chinese). Seeds produced by da2-1 were larger and heavier than the wild-type seeds (FIGS. 1A, 3C and 3D). Seed number per silique and seed yield per plant in da2-1 were slightly higher than those in wild type (FIGS. 1B and 1C). By contrast, total number of seeds per plant in da2-1 was not significantly increased, compared with that in wild type (FIG. 1D). The da2-1 plants were higher than wild-type plants at the mature stage (FIG. 1E). In addition, da2-1 mutant plants formed large flowers and leaves as well as increased biomass compared with wild-type plants (FIG. 2 ; FIG. 15 ). The increased size of da2-1 mutant petals and leaves was not caused by larger cells (FIG. 15 ), indicating that it is the number of petal and leaf cells that is higher.

2.2 DA2 Acts Synergistically with DA1 to Control Seed Size, but does so Independently of EOD1

The da2-1 mutant showed a weak but similar seed size phenotype to da1-1 (Li et al., 2008), providing indication that DA1 and DA2 could function in a common pathway. To test for a genetic interaction between DA1 and DA2, we generated a da1-1 da2-1 double mutant and determined its seed size. Although the da2-1 mutant had slightly larger and heavier seeds than wild type (FIGS. 1A, 3C and 3D), the da2-1 mutation synergistically enhanced the seed size and weight phenotypes of da1-1 (FIGS. 3A and 3C), revealing a synergistic genetic interaction between DA1 and DA2 in seed size. The changes in seed size were reflected in the size of the embryos and resulting seedlings (FIG. 3B). We further measured cotyledon area of 10-d-old seedlings. A synergistic enhancement of cotyledon size of da1-1 by the da2-1 mutation was also observed (FIGS. 3B and 4). The mutant protein encoded by the da1-1 allele has a negative activity toward DA1 and a DA1-related protein (DAR1), the most closely-related family member (Li et al., 2008).

Double da1-ko1 dar1-1 T-DNA insertion mutants exhibited the da1-1 phenotypes, while da1-ko1 and dar1-1 single mutants did not show an obvious seed size phenotype (Li et al., 2008). As da1-1 and da2-1 act synergistically to increase seed size, one would expect that the da1-ko1 might synergistically enhance the phenotypes of da2-1. To test this, we generated the da1-ko1 da2-1 double mutant. As shown in FIG. 3D, the seed size and weight phenotypes of da2-1 were also synergistically enhanced by the da1-ko1 mutation. We further measured cotyledon area of 10-d-old seedlings. The da1-ko1 mutation synergistically enhanced the cotyledon size phenotype of da2-1 (FIG. 4 top right). Similarly, a synergistic enhancement of petal size of da2-1 by the da1-ko1 mutation was also observed (FIG. 16A). These results further demonstrate the synergistic effects of the simultaneous disruption of both DA1 and DA2.

We further measured the size of embryo cells and petal epidermal cells. Cell size in da1-1 da2-1 and da1-ko1 da2-1 double mutants was not increased, compared with that measured in their parental lines (FIG. 4 lower left; FIG. 16B), providing indication that DA1 and DA2 act synergistically to restrict cell proliferation processes.

The da1-1 da2-1 double mutant had larger seeds than da1-ko1 da2-1 double mutants (FIGS. 3C, 3D and 4 ), which is consistent with our previous report that the da1-1 allele had stronger phenotypes than da1-ko1 (Li et al.,2008). The size of da1-1 seeds was similar to that of da1-ko1 dar1-1 double mutant seeds because the da1-1 allele has a negative activity toward DA1 and DAR1 (FIG. 4 lower right) (Li et al., 2008). Therefore, one would expect that the size of da1-1 da2-1 double mutant seeds might be similar to that of da1-ko1 dar1-1 da2-1 triple mutant seeds. We therefore generated a da1-ko1 dar1-1 da2-1 triple mutant and investigated its seed size. As shown in FIG. 4 , the size of da1-ko1 dar1-1 da2-1 triple mutant seeds was comparable with that of da1-1 da2-1 double mutant seeds, but larger than that of da1-ko1 da2-1 double mutant seeds. Thus, these genetic analyses further support that the da1-1 allele has a negative effect on both DA1 and DAR1 (Li et al., 2008).

We have previously identified an enhancer of da1-1 (EOD1), which is allelic to BIG BROTHER (BB) (Disch et al., 2006; Li et al., 2008). The eodl mutations synergistically enhanced the seed size phenotype of da1-1 (Li et al., 2008). Similarly, the seed size and weight phenotypes of da2-1 were synergistically enhanced by da1-1 and da1-ko1 (FIGS. 3A,3C and 3D). We therefore asked whether DA2 and EOD1 could function in a common pathway. To determine genetic relationships between DA2 and EOD1, we analyzed an eod1-2 da2-1 double mutant. The genetic interaction between eod1-2 and da2-1 was essentially additive for both seed weight and petal size compared with their parental lines (FIG. 16 ), providing indication that DA2 functions to influence seed and organ growth separately from EOD1.

2.3 DA2 Acts Maternally to Influence Seed Size

Considering that the size of seeds is affected by the maternal and/or zygotic tissues, we asked whether DA2 functions maternally or zygotically. To test this, we performed reciprocal cross experiments between wild type and da2-1. As shown in FIG. 6 , the effect of da2-1 on seed size was observed only when maternal plants are homozygous for the da2-1 mutation. Seeds produced by maternal da2-1 plants, regardless of the genotype of the pollen donor, were consistently larger than those produced by maternal wild-type plants. This result indicates that da2-1 can act maternally to influence seed size. We have previously demonstrated that DA1 also functions maternally to control seed size (Li et al. 2008). As the da1-ko1 mutation synergistically enhanced the seed size phenotype of da2-1 (FIG. 3D), we further conducted reciprocal cross experiments between wild type and da1-ko1 da2-1 double mutant Similarly, the effect of da1-ko1 da2-1 on seed size was observed only when da1-ko1 da2-1 acted as the maternal plant (FIG. 6 ).

Pollinating dal-ko1/+da2-1/+plants with da1-ko1 da2-1 double mutant pollen leads to the development of da1-ko1 da2-1, da1-ko1/da1-ko1 da2-1/+, dal-ko1/+da2-1da2-1 and dal-ko1/+da2-1/+embryos within dal-ko1/+da2-1/+seed coats. We further measured the size of individual seeds from dal-ko1/+da2-1/+plants fertilized with da1-ko1 da2-1 double mutant pollen and genotyped da1-ko1 and da2-1 mutations. Our results show that da1-ko1 and da2-1 mutations are not associated with variation in the size of these seeds (FIG. 6 ). Together, these analyses indicate that the embryo and endosperm genotypes for DA1 and DA2 do not affect seed size, and DA1 and DA2 are required in sporophytic tissue of the mother plant to control seed growth.

2.4 DA2 Acts Synergistically with DA1 to Affect Cell Proliferation in the Maternal Integuments

The reciprocal crosses showed that DA1 and DA2 function maternally to determine seed size (FIG. 6 ) (Li et al., 2008). The integuments surrounding the ovule are maternal tissues and form the seed coat after fertilization, which may physically restrict seed growth. Several studies showed that the integument size of ovules determines seed size (Schruff et al., 2006; Adamski et al., 2009). We therefore asked whether DA1 and DA2 act through the maternal integuments to control seed size. To test this, we investigated mature ovules from wild type, da1-1,da2-1 and da1-1 da2-1 at 2 days after emasculation. The size of da1-1 ovules was dramatically larger than that of wild-type ovules (FIGS. 5 and 7 ), consistent with our previous findings (Li et al., 2008).

The da2-1 ovules were also larger than wild-type ovules (FIGS. 5, and 7 ). The da2-1 mutation synergistically enhanced the ovule size phenotype of da1-1, consistent with their synergistic interactions in seed size.

We investigated the outer integument cell number of developing seeds in wild type, da1-1, da2-1 and da1-1 da2-1 at 6 DAP and 8 DAP. In wild-type seeds, the number of outer integument cells at 6 DAP was similar to that at 8 DAP (FIG. 7 middle panel), indicating that cells in the outer integuments of wild-type seeds completely stop division at 6 DAP. Similarly, cells in the outer integuments of da1-1, da2-1 and da1-1 da2-1 seeds completely stopped cell proliferation at 6 DAP. The number of outer integument cells in da1-1 and da2-1 seeds was significantly increased compared with that in wild-type seeds (FIG. 7 ). The da2-1 mutation synergistically enhanced the outer integument cell number of da1-1. We further investigated the outer integument cell length of wild-type, da1-1, da2-1 and da1-1 da2-1 seeds at 6 and 8 days after pollination. Cells in da1-1, da2-1 and da1-1 da2-1 outer integuments were significantly shorter than those in wild-type outer integuments (FIG. 7 right panel), providing indication of a compensation mechanism between cell proliferation and cell expansion in the integuments. Thus, these results show that DA2 acts synergistically with DA1 to restrict cell proliferation in the maternal integuments.

2.5 DA2 Encodes a Functional E3 Ubiquitin Ligase

The da2-1 mutation was identified with T-DNA insertion in the seventh exon of the gene At1g78420 (FIG. 8A). The T-DNA insertion site was further confirmed by PCR using T-DNA specific and flanking primers and sequencing PCR products. The full-length mRNA of At1g78420 could not be detected by semi-quantitative RT-PCR in da2-1 mutant. We expressed the At1g78420 CDS under the control of its own promoter in da2-1 plants and isolated 62 transgenic plants. Nearly all transgenic lines exhibited complementation of da2-1 phenotypes (FIG. 10 ), indicating that At1g78420 is the DA2 gene.

To further characterize DA2 function, in particular gain of function phenotypes, we expressed the coding region of DA2 under the control of the CaMV 35S promoter in wild-type plants and isolated 77 transgenic plants. Overexpression of DA2 caused decreases in seed size, seed yield per plant and seed number per plant (FIGS. 1A, 1C and 1D). In addition, most transgenic plants overexpressing DA2 had small flowers and leaves, short siliques, reduced plant height as well as decreased biomass compared with wild type (FIGS. 1E, 2 and 15 ). These results further support the role of DA2 in limiting seed and organ growth.

The DA2 gene is predicted to encode a 402 -amino-acid protein containing one predicted RING domain (59-101) (FIG. 8B; Table 1). To investigate whether DA2 has E3 ubiquitin ligase activity, we expressed DA2 in Escherichia coli as a fusion protein with maltose binding protein (MBP) and purified MBP-DA2 protein from the soluble fraction. In the presence of an El ubiquitin activating enzyme, an E2 conjugating enzyme, His-ubiquitin and MBP-DA2, a polyubiquitination signal was observed by western blot using an anti-His antibody (FIG. 9 , fifth lane from the left). The anti-MBP blot analysis also showed that MBP-DA2 was ubiquitinated (FIG. 9 , fifth lane from the left). However, in the absence of any of El, E2, His-ubiquitin or MBP-DA2, no polyubiquitination was detected (FIG. 9 , first to fourth lanes from the left), demonstrating that DA2 is a functional E3 ubiquitin ligase. The RING motif is essential for the E3 ubiquitin ligase activity of RING finger proteins (Xie et al., 2002). Therefore, we tested whether an intact RING finger domain was required for DA2 E3 ligase activity. A single amino acid substitution allele was produced by mutagenizing Cysteine-59 to Serine (C59S), as this mutation is predicted to disrupt the RING domain (Tables 1 and 2). An in vitro ubiquitination assay indicated that the E3 ligase activity was abolished in the C59S mutant of DA2 (FIG. 9 , sixth lane from the left), indicating that an intact RING domain is required for DA2 E3 ubiquitin ligase activity. We further overexpressed DA2 C59S (35S:DA2C59S) in wild-type Col-0 plants and isolated 69 transgenic plants. The seed size of transgenic plants was comparable with that of wild-type plants although transgenic plants had high expression levels of DA2 C59S, indicating that the DA2 C59S mutation affects the function of DA2 in seed growth.

Three RING types, RING-H2, RING-HCa and RING-HCb, and five modified RING types, RING-C2, RING-v, RING-D, RING-S/T and RING-G have been described in Arabidopsis (Stone et al., 2005). A new type of RING domain (C5HC2) found in rice GW2 has been proposed (Song et al., 2007). Although the spacing of the cysteines in the predicted RING domain of DA2 was similar to that in the RING domain (C5HC2) of rice GW2, the RING domain of DA2 lacked a conserved histidine residue that was replaced by an asparagine residue (Asn-91) (Tables 1 and 2). This amino acid substitution was also observed in the predicted RING domain of DA2 homologs in dicots, such as soybean and oilseed rape (Table 1). We therefore asked whether this asparagine residue (Asn-91) is crucial for its E3 ubiquitin ligase activity. A single amino acid substitution allele was produced by mutagenizing Asn-91 to Leucine (N91L). An in vitro ubiquitination assay showed that the N91L mutant of DA2 had the E3 ligase activity (FIG. 9 , the seventh lane from the left), suggesting that Asn-91 may not be required for DA2 E3 ligase activity. These results suggest that the RING domain of DA2 might be a variant of that found in GW2. We further overexpressed DA2 N91L (35S:DA2N91L) in wild-type plants and isolated 26 transgenic plants. The seeds of transgenic plants were smaller than wild-type seeds, suggesting that the DA2 N91L could restrict seed growth.

2.6 Homologs of Arabidopsis DA2

Proteins that share significant homology with DA2 outside of the RING domain are found in Arabidopsis and crop plants including oilseed rape, soybean, rice, maize and barley (Table 2). One predicted protein in Arabidopsis shares extensive amino acid similarity with DA2 and is named DA2-like protein (DA2L; At1g17145). Like 35S:DA2 plants, DA2L-overexpressing lines exhibited small plants and organs (FIG. 18 ), providing indication that DA2 and DA2L have similar functions. The similar proteins in other plant species show a 39.2%-84.5% amino acid sequence identity with DA2 (Table 2). The homolog in Brassica napus had the highest amino acid sequence identity with DA2 (84.5%) (Table 2). Rice GW2 had 43.1% amino acid sequence identities with Arabidopsis DA2 (Table 2). As overexpression of GW2 reduced grain width in rice (Song et al., 2007), we asked whether DA2 and GW2 performs similar function in seed size control. We therefore overexpressed GW2 in wild-type plants. Like 35S:DA2 and 35S:DA2L transgenic lines, the Arabidopsis transgenic plants overexpressing GW2 produced smaller seeds and organs than wild-type plants, indicating conserved function for Arabidopsis DA2 and rice GW2 in seed and organ growth control.

2.7 DA2 and DA1 show Similar Expression Patterns

To determine the expression pattern of DA2, RNAs from roots, stems, leaves, seedlings and inflorescences were analyzed by quantitative real-time RT-PCR analysis. DA2 mRNA was detected in all plant organs tested (FIG. 11 , panel A). The tissue-specific expression patterns of DA2 were investigated using histochemical assay of GUS activity of transgenic plants containing a DA2 promoter:GUS fusion (pDA2: GUS). GUS activity was detected in roots, cotyledons, leaves and inflorescences (FIG. 11 , panels B and C). Relatively high GUS activity was detected in leaf primordia and roots (FIG. 11 , panels B and C). In flowers, relatively stronger expression of DA2 was observed in young floral organs than old floral organs (FIG. 11 , panels D-L). Similarly, higher GUS activity was detected in younger ovules than older ones (FIG. 11 , panels M and N). This shows that DA2 expression is regulated temporally and spatially.

2.8 DA1 Interacts with DA2 In Vitro and In Vivo

Our genetic analyses show that DA1 acts synergistically with DA2 to restrict seed and organ growth. We therefore assessed whether DA1 interacts with the E3 ubiquitin ligase DA2 using an in vitro interaction/pull-down experiment. DA1 was expressed as a GST fusion protein, while DA2 was expressed as a MBP fusion protein. As shown in FIG. 12 (first and second lanes from left), GST-DA1 bound to MBP-DA2, while GST-DA1 did not bind to a negative control (MBP). This result indicates that DA1 physically interacts with DA2 in vitro.

DA1 contains two ubiquitin interaction motifs (UIM), a single LIM domain and the highly conserved C-terminal region (FIG. 13 ) (Li et al., 2008). We further asked which domain of DA1 is required for interaction between DA1 and DA2. A series of DA1 derivatives containing specific protein domains were expressed in Escherichia coli: DA1-UIM containing only the two UIM domains, DA1-LIM with only the LIM domain, DA1-LIM+C containing only the LIM domain and the C-terminal region, and DA1-C with only the C-terminal region, were expressed as GST fusion proteins (FIG. 13 ).

DA2 was expressed as an MBP fusion protein and used in pull-down experiments. As shown in FIG. 12 , GST-DA1-LIM+C and GST-DA1-C interacted with MBP-DA2, but the GST-DA1-UIM and GST-DA1-LIM did not bind to MBP-DA2. This result indicates that the conserved C-terminal region of DA1 interacts with DA2.

Considering that the mutant protein encoded by the da1-1 allele (DA1R358K) has a mutation in the C-terminal region (FIG. 13 ) (Li et al., 2008), we asked whether the DA1R358K mutation affects interactions with DA2. Using a GST-DA1R358K fusion protein in pull-down experiments with MBP-DA2, we showed that the mutation in DA1R358K does not affect the interaction between DA1 and DA2 (FIG. 12 , third lane from left).

To further investigate possible association between DA1 and DA2 in planta, we used coimmunoprecipitation analysis to detect their interactions in vivo. We transiently coexpressed 35S:Myc-DA1 and 35S:GFP-DA2 in Nicotiana benthamiana leaves. Transient coexpression of 35S:GFP and 35S:Myc-DA1 in Nicotiana benthamiana leaves was used as a negative control. Total proteins were isolated and incubated with GFP-Trap-A agarose beads to immunoprecipitate GFP-DA2 or GFP. Precipitates were detected with anti-GFP and anti-Myc antibodies, respectively. As shown in FIG. 14 , Myc-DA1 was detected in the immunoprecipitated GFP-DA2 complex but not in the negative control (GFP), indicating that there is a physical association between DA1 and DA2 in planta. As the C-terminal region of DA1 interacted with DA2 in the pull-down assay (FIG. 12 ), we further asked whether the C-terminus of DA1 interacts with DA2 in planta. The co-immunoprecipitation analysis showed that the C-terminal region of DA1 (Myc-DA1-C) was detected in the GFP-DA2 complex but not in the negative control (PEX10-GFP, a RING-type E3 ubiquitin ligase) (Platta et al., 2009; Kaur et al., 2013). Thus, these results indicate that the C-terminal region of DA1 is required for interaction with DA2 in vitro and in vivo.

Seed size in higher plants is a key determinant of evolutionary fitness, and is also an important agronomic trait in crop domestication (Gomez, 2004; Orsi and Tanksley, 2009). Several factors that act maternally to control seed size have been identified, such as ARF2/MNT, AP2, KLU/CYP78A5, EOD3/CYP78A6 and DA1. However, the genetic and molecular mechanisms of these factors in seed size control are nearly totally unknown. We previously demonstrated that the ubiquitin receptor DA1 acts synergistically with the E3 ubiquitin ligase EOD1/BB to control seed size (Li et al., 2008).

In this study, we identified Arabidopsis DA2 as another RING E3 ubiquitin ligase involved in controlling seed size. Genetic analyses show that DA2 functions synergistically with DA1 to control final seed size, but does so independently of the E3 ubiquitin ligase EOD1. We further revealed that DA1 interacts physically with DA2. Our results define a ubiquitin-based system involving DA1, DA2 and EOD1 that controls final seed size in Arabidopsis.

2.9 DA2 Acts Maternally to Control Seed Size

The da2-1 loss-of-function mutant formed large seeds and organs, whereas plants overexpressing DA2 produced small seeds and organs (FIG. 1A), indicating that DA2 is a negative factor of seed and organ size control. Surprisingly, Arabidopsis DA2 has been recently proposed as a positive regulator of organ growth, although nothing is known about how DA2 controls seed and organ growth (Van Daele et al., 2012). In this study, we have sufficient evidence to prove that DA2 acts as a negative factor of seed and organ growth control. The da2-1 loss-of-function mutant formed large seeds and organs (FIGS. 1 to 4 ). Supporting this, the da2-1 mutation synergistically enhanced the seed and organ size phenotypes of da1-1 and da1-ko1 (FIGS. 1 to 4 ). The da2-1 mutation also enhanced the seed and organ size phenotypes of eod1-2, further indicating that the da2-1 mutation promotes seed and organ growth. The da2-1 mutant formed large ovules with more cells in the integuments, and the da2-1 mutation synergistically enhanced the ovule size phenotype of da1-1 (FIG. 6 ).

In addition, most transgenic plants overexpressing DA2 and DA2L were smaller than wild-type plants (FIG. 2 ). The organ growth phenotypes of these transgenic plants were correlated with their respective expression levels. Therefore, our data clearly demonstrate that DA2 functions as a negative regulator of seed and organ size. Several Arabidopsis mutants with large organs also formed large seeds (Krizek, 1999; Mizukami and Fischer, 2000; Schruff et al., 2006; Li et al., 2008; Adamski et al., 2009), suggesting a possible link between organ size and seed growth. By contrast, several other mutants with large organs exhibited normal sized seeds (Hu et al., 2003; White, 2006; Xu and Li, 2011), indicating that organ and seed size is not invariably positively related. These results suggest that seeds and organs have both common and distinct pathways to control their respective size.

Reciprocal cross experiments showed that DA2 acts maternally to influence seed growth, and the embryo and endosperm genotypes for DA2 do not affect seed size (FIG. 6 ). The integuments surrounding the ovule are maternal tissues and form the seed coat after fertilization. Alterations in maternal integument size, such as those seen in arf2, da1-1 and klu ovules, have been known to contribute to changes in seed size (Schruff et al., 2006; Li et al., 2008; Adamski et al., 2009). Mature da2-1 ovules were larger than mature wild-type ovules (FIGS. 5 and 7 ). The da2-1 mutation also synergistically enhanced the integument size of da1-1 ovules. Thus, a general theme emerging from these studies is that the control of maternal integument size is one of key mechanisms for determining final seed size. Consistent with this notion, plant maternal factors of seed size control (e.g. KLU, ARF2 and DA1) isolated to date influence integument size (Schruff et al., 2006; Li et al., 2008; Adamski et al., 2009).

The size of the integument or seed coat is determined by cell proliferation and cell expansion, two processes that are coordinated. Cell number in the integuments of the mature ovule sets the growth potential of the seed coat after fertilization. For example, arf2 mutants produced large ovules with more cells, leading to large seeds (Schruff et al. 2006), while klu mutants had small ovules with less cells, resulting in small seeds (Adamski et al., 2009). Our results show that the integuments of da1-1 and da2-1 seeds had more cells than those of wild-type seeds, and da1-1 and da2-1 acts synergistically to promote cell proliferation in the integuments (FIG. 7 ). We also observed that cells in the outer integuments of da1-1, da2-1, and da1-1 da2-1 seeds were shorter than those in wild-type integuments (FIG. 7 ), suggesting that a possible compensation mechanism between cell proliferation and cell elongation in the maternal integument. Thus, it is possible that the maternal integument or seed coat, which acts as a physical constraint on seed growth, can set an upper limit to final seed size.

2.10 A Genetic Framework for Ubiquitin-Mediated Control of Seed Size

DA2 encodes a protein with one predicted RING domain that is distinctive from any of the previously described plant RING domains. The RING domain of DA2 shared highest homology with that of rice GW2 (C5HC2), but it lacked one conserved metal ligand amino acid (a histidine residue) that was replaced by an asparagine residue (Song et al., 2007). It is still possible that the RING domain of DA2 might be a variant of that found in GW2. Many RING-type domains are found in E3 ubiquitin ligases that ubiquitinate substrates, often targeting them for subsequent proteasomal degradation (Smalle and Vierstra, 2004). We tested the E3 activity of recombinant DA2 in an in vitro ubiquitin-ligase assay and demonstrated that DA2 is a functional E3 ubiquitin ligase (FIG. 9 ), suggesting that DA2 may target positive regulators of cell proliferation for ubiquitin-dependent degradation by the 26S proteasome. Proteins that share homology with DA2 outside the RING domain are found in Arabidopsis and other plant species. In Arabidopsis, the DA2-like protein (DA2L) shares extensive amino acid similarity with DA2. Like 35S:DA2 plants, DA2L-overexpres sing lines showed small plants (FIG. 18 ), indicating that DA2 and DA2L may perform similar functions. The homolog of DA2 in rice is the RING-type (C5HC2) protein GW2 (Song et al., 2007), which has been known to act as a negative regulator of seed size. However, the genetic and molecular mechanisms of GW2 in seed size control are largely unknown in rice.

We previously identified DA1, a ubiquitin receptor with ubiquitin-binding activity, as a negative regulator of seed size (Li et al., 2008). A modifier screen identified an enhancer of da1-1 (EOD1) (Li et al., 2008), which is allelic to the E3 ubiquitin ligase BB (Disch et al., 2006). Analysis of double eod1-2 da1-1 mutants revealed synergistic genetic interactions between DA1 and EOD1 (Li et al., 2008), suggesting they may control seed growth by modulating the activity of a common target(s). Although genetic interactions between da1-1 and eod1-2 also synergistically enhanced seed and organ size, our genetic analyses show that DA2 acts independently of EOD1 to influence seed growth, suggesting DA2 and EOD1 may target distinct growth stimulators for degradation, with common regulation via DA1. Thus, our findings establish a framework for the control of seed and organ size by three ubiquitin-related proteins DA1, DA2 and EOD1. In addition, we observed that overexpression of GW2 restricts seed and organ growth in Arabidopsis, providing indication of a possible conserved function in Arabidopsis and rice. It could be interesting to investigate the effects of the combination of GW2 and rice homologs of DA1 and EOD1 on grain size in rice.

2.11 A Possible Molecular Mechanism of DA1 and DA2 in Seed Size Control

Our results demonstrate that the E3 ubiquitin ligase DA2 interacts with the ubiquitin receptor DA1 in vitro and in vivo (FIGS. 12-14 ). However, it is not likely that DA2 targets DA1 for proteasomal degradation because a T-DNA inserted mutant of the DA1 gene (dal -ko1) synergistically enhances the seed size phenotype of da1-1 (FIGS. 3 and 4 ). Nevertheless, many other types of ubiquitin modification regulate proteins in a proteasome independent manner (Schnell and Hicke, 2003). For example, monoubiquitination has been implicated in the activation of signaling proteins, endocytosis, and histone modification (Schnell and Hicke, 2003). In animals, monoubiquitination of the ubiquitin receptor eps15 depends on interaction between eps15 and the Nedd4 family of E3 ligases (Woelk et al., 2006). In contrast, an E3-independent monoubiquitination of ubiquitin receptors has also been reported (Hoeller et al., 2007). Considering that DA1 interacts with DA2, we tested whether DA2 can ubiquitinate or monoubiquitinate DAL In the presence of El, E2 and ubiquitin, DA2-His had an E3 ubiquitin ligase activity. However, in the presence of El, E2, ubiquitin and DA2-His (E3), no ubiquitinated DA1-HA was detected under our reaction conditions. Ubiquitin receptors can interact with polyubiquitinated substrates of E3s via UIM domains and facilitate their degradation by the proteasome (Verma et al., 2004). We previously demonstrated that UIM domains of DA1 can bind ubiquitin (Li et al., 2008).

Taken together with its interaction with DA2 through its C-terminal region (FIGS. 12 and 14 ), DA1 may be involved in mediating the degradation of the ubiquitinated substrates of DA2 by the proteasome. One mechanism may involve DA1 interaction with DA2, which helps DA1 specifically recognize the ubiquitinated substrate(s) of DA2. DA1 may subsequently bind polyubiquitin chains of the ubiquitinated substrate(s) through its UIM domain and mediate the degradation of the ubiquitinated substrate(s). Improving seed yield is an important target for crop breeders worldwide, and the size of seeds is an important component of overall seed yields. We identified DA2 as an important regulator of seed size that functions synergistically with DA1 to influence seed size.

DA1 also acts synergistically with EOD1 to affect seed growth. Overexpression of a dominant negative da1-1 mutation (Zmda1-1) has been reported to increase seed mass of corn (Wang et al., 2012), indicating the promise of combining the effects of DA1, DA2 and EOD1 from different seed crops to engineer large seed size in these crops.

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TABLE 1 Alignment of DA2 RING domains (SEQ ID NOS: 3-19) Bd_Bradi3g09270 CPICFLYYPSLNRSKCCSKGICTECFLQMKPTHTARPTQCPFC Hv_Yrg1 CPICFLYYPSLNRSKCCSKGICTECFLQMKPTHTARPTQCPFC Zm_gi|220961719 CPICFLYYPSLNRSKCCSKGICTECFLQMKPTHTARPTQCPFC Sb_gi|242064618 CPICFLYYPSLNRSKCCSKGICTECFLQMKPTHTARPTQCPFC Os_GW2 CPICFLYYPSLNRSKCCSKGICTECFLQMKPTHTAQPTQCPFC Pt_gi|224061326 CPICFLYYPSLNRSRCCMKGICTECFLQMKNPNSTRPTQCPFC Cp_evm.model.supercontig 77 CPICFLYYPSLNRSRCCMKGICTECFLQMKNPNSTRPTQCPFC Rc_gi|255578534 CPICFLYYPSLNRSRCCMKGICTECFLQMKNPNSTRPTQCPFC At_DA2 CPICFLYYPSLNRSRCCMKSICTECFLQMKNPNSARPTQCPFC Bn_DA2 CPICFLYYPSLNRSRCCMKSICTECFLQMKNPNSARPTQCPFC At_DA2L CPICFLYYPSLNRSRCCMKSICTECFLRMKSPNSAQPTQCPFC Gm_Glyma 13g33260.1 CPICFLYYPSLNRSRCCTKSICTECFLQMKVPNSTRPTQCPFC Sb_Sb10g003820 CPICFLFYPSLNRSKCCAKGICTECFLQMKSPTSCRPTQCPYC Bd_Bradi1g49080 CPICFLFYPSLNRSKCCAKGICTECFLQMKSPTSCRPTQCPYC Zm_gi|260935347 CPICFLFYPSLNRSKCCAKGICTECFLQMKSPTSCKPTQCPYC Os_gi|218197613 CPICFLFYPSLNRSKCCAKGICTECFLQMRTPTSCRPTQCPYC Vv_DA2 CPICFLFYPSLNRSRCCTKGICTECFLQMKNPNSTRPTQCPYC ↑  ↑            ↑    ↑  ↑       ↑      ↑  ↑ C  C            C    C  C     H/N/T    C  C

TABLE 2 Alignment of DA2 polypeptides (SEQ ID NOS: 20-35) Pt_GI-224061326.pro MGNKLG---RRRQVVDERYTRPQGLYVHKDVDHKKLRKLILESKIAPCFPGDEDSCND--  55 Rc_GI-255578534.pro MGNKLG---RRRQVVDERYTRPQGLYVHKDVDHKKLRKLILESKLAPCYPGDDEFGND--  55 Vv_GI-147817790.pro MGNKLG---RRRQVVEDKYTRPQGLYQHKDVDHKKLRKLILDSKLAPCYPGDEEATND--  55 Gm_GI-356549538 pro MGNKLG---RRRQVVDEKYTRPQGLYNHKDVDHKKLRKLILESKLAPCYPGDEETAYD--  55 At_GI-18411948.pro MGNKLG---RKRQVVEERYTKPQGLYVNKDVDVKKLRKLIVESKLAPCYPGDDESCHD--  55 Ta_GI-408743661.pro MGNRIGG--RRKAGVEERYTRPQGLYEHRDIDQKKLRKLILEAKLAPCYPGADDAAGG--  56 Hv_GI-164371454.pro MGNRIGG--RRKAGVEERYTRPQGLYEHRDIDQKKLRKLILETKLAPCYPGADDAAGA--  56 Bd_GI-357140854.pro MGNRIGG--RRKAGVEERYTRPQGLYEHRDIDQKKLRKLILEAKLAPCYPGADDAAGG--  56 Os_GI-115445269.pro MGNRIGG--RRKAGVEERYTRPQGLYEHRDIDQKKLRKLILEAKLAPCYMGADDAAAAA-  57 Sb_GI-242064618.pro MGNRKGG--RPKSGGEKRFTPPQGLYEHKDIDQKKLRKLILEAKLAPCYPGADDAAAAGG  58 Zm_GI-220961719.pro MGNRIGG--RRKPGVEERFTRPQGLYEHKDIDQKKLRKLILEAKLAPCYPGADDAAAGGG  58 Ta_GI-408743658.pro MGNRIGG--RRKAGVEERYTRPQGLYEHRDIDQKKLRKLILEAKLAPCYPGADDAAGG--  56 Bd_GI-357125256.pro MGN-------------------QGLYFHFDIDKKLRRLIVEAKLAFCHPGSIDDPRAD--  39 Os_GI-218197613.pro MGNQVGGRRRRRPAVEERYTRPQGLYPHPDIDLKKLRRLIVEAKLAPCFPGSDDPRAD--  58 Zm_GI-260935347.pro MGNQVGGRRRRRPPVDERYTRPQGLYPHPDIDLRKLRRLILEAKLAPCHPGADDARAD--  58 Sb_GI-242092026.pro MGNQVGGRRRRRPAVDERYTQPQGLYPHPDIDLRKLRRLILEAKLAPCHPGADDARAD--  58 ***                   **** : *:* :***:**:::*****. * :: Pt_GI-224061326.pro ---HEECPICFLYYPSLNRSRCCMKGICTECFLQMKNPNSTRPTQCPFCKTSNYAVEYRG 112 Rc_GI-255578534.pro ---HEECPICFLYYPSLNRSRCCMKGICTECFLQMKNPNSTRPTQCPFCKTTNYAVEYRG 112 Vv_GI-147817790.pro ---FEECPICFLFYPSLNRSRCCTKGICTECFLQMKNPNSTRPTQCPYCKTANYAVEYRG 112 Gm_GI-356549538 pro ---REECPICFLYYPSLNRSRCCTKSICTECFLQMKVPNSTRPTQCPFCKTANYAVEYRG 112 At_GI-18411948.pro ---LEECPICFLYYPSLNRSRCCMKSICTECFLQMNNPNSARPTQCPFCKTPNYAVEYRG 112 Ta_GI-408743661.pro --DLEECPICFLYYPSLNRSKCCSKGICTECFLQMKPTHTARPTQCPFCKTPNYAVEYRG 114 Hv_GI-164371454.pro --DLEECPICFLYYPSLNRSKCCSKGICTECFLQMKPTHTARPTQCPFCKTPNYAVEYRG 114 Bd_GI-357140854.pro --DLEECPICFLYYPSLNRSKCCSKGICTECFLQMKPTHTARPTQCPFCKTPNYAVEYRG 114 Os_GI-115445269.pro --DLEECPICFLYYPSLNRSKCCSKGICTECFLQMKPTHTAQPTQCPFCKTPSYAVEYRG 115 Sb_GI-242064618.pro --DLEECPICFLYYPSLNRSKCCSKGICTECFLQMKPTHTARPTQCPFCKTPNYAVEYRG 116 Zm_GI-220961719.pro DLDLEECPICFLYYPSLNRSKCCSKGICTECFLQMKPTHTARPEQCPFCKTANYAVEYRG 118 Ta_GI-408743658.pro --DLEECPICFLYYPSLNRSKCCSKGICTECFLQMKPTHTARPTQCPFCKTPNYAVEYRG 114 Bd_GI-357125256.pro ---LDECPICFLFYPSLNRSKCCAKGICTECFLQMKSPTSCRPTQCPYCKMLNYAVEYRG  96 Os_GI-218197613.pro ---LEECPICFLFYPSLNRSKCCAKGICTECFLQMRTPTSCRPTQCPYCKMASYAVEYRG 115 Zm_GI-260935347.pro ---LDECPICFLFYPSLNRSKCCAKGICTECFLQMKSPTSCKPTQCPYCKTLNYAVEYRG 115 Sb_GI-242092026.pro ---LDECPICFLFYPSLNRSKCCAKGICTECFLQMKSPTSCRPTQCPYCKTLNYAVEYRG 115     :*******:*******:** *.*********: . : :*****:**  .******* Pt_GI-224061326.pro VKTKEEKGLEQIEEQRVIEAKIRMRQQELQDEEERMQKRLDVSSSSANIEPG-ELECGPT 171 Rc_GI-255578534.pro VKTKEEKGMEQIEEQRVIEAKIRMRQQELQDEEERMQKRLELSSSSSSIAPG-EVECGSA 171 Vv_GI-147817790.pro VKTKEEKGMEQIEEQRVIEAKIRMRQKEIQDEEERMQKRQEISSSSSILAQG-EVEYSTT 171 Gm_GI-356549538 pro VKSKEEKGLEQIEEQRVIEAKIRMRQQELQDEEERMHKRLEMSSSNVNVAVA-DVEYSSN 171 At_GI-18411948.pro VKSKEEKGIEQVEEQRVIEAKIRMRQKEMQDDEEKMQKRLESCSSSTSAMTG-EMEYGST 171 Ta_GI-408743661.pro VKTKEERSIEQFEEQKVIEAQMRMRQQALQDEEDKMKRKQSRCSSSRTIAPTTEVEYRDI 174 Hv_GI-164371454.pro VKTKEERSIEQFEEQKVIEAQMRMRQQALQDEEDKMRRKQSRCSSSRTIAPTTEVEYRDI 174 Bd_GI-357140854.pro VKTKEERSIEQLEEQKVIEAQMRMRQQALQDEEDKMRRKQSRCSSSRTIAPTTEVEYRDI 174 Os_GI-115445269.pro VKTKEERSIEQFEEQKVIEAQMRMRQQALQDEEDKMKRKQNRCSSSRTITPTKEVEYRDI 174 Sb_GI-242064618.pro VKTKEERSIEQFEEQKVIEAQLRMRQKELQDEEAKMKRKQCRCSSSRTVTPTTEVEYRDI 175 Zm_GI-220961719.pro VKTKEERSIEQFEEQKVIEAQLRMRQKELQDEEAKMKRKQSRCSSSRTVTPTTEVEYRDI 176 Ta_GI-408743658.pro VKTKEERSIEQFEEQKVIEAQLRMRQKELQDEEAKMKRKQSRCSSSRTVTPTTEVEYRDI 178 Bd_GI-357125256.pro VKTKEEKGVEQLEEQRVIEAQIRMRHQEIKDDAERLKNKQ--TATLSDVITTPQVECCEA 173 Os_GI-218197613.pro VKTKEEKGTEQIEEQRVIEAQIRMRQQELQDDAERMKKKQ--AAALTDVVTTAQVEHCDT 154 Zm_GI-260935347.pro VKTKEEKGIEQLEEQRVIEAQIRMRQQEVQDDAERMKNKR--TATLGDVVASAQVDSCNT 173 Sb_GI-242092026.pro VKTKEEKGIEQLEEQRVIEAQIRMRQKELQDDAERMKNKQ--TATLGDIVASAQVDSCNT 173 **:***:. **.***:****::*:*:: ::*:  :::.:    ::          :: Pt_GI-224061326.pro TVPS-DTTPVE-------SGEIVSSQYS-----SRRPPHAGANRDDEFDLDLEDIMVMEA 218 Rc_GI-255578534.pro AVQS-FRSPLE-------AEGSIPSQFS-----IRHPPHYRANRDDEFDLDLEDIMVMEA 218 Vv_GI-147817790.pro AVPS-FRSPVE-------GDEIDSSQDPRAASMIIQTLPPRQNRDEEFDLDLEDIMVMEA 223 Gm_GI-356549538 pro AVSSSSVSVVE-------NDEIVSSQDSCATSVVRANATTRTNRDDEFDVDLEDIMVMEA 224 At_GI-18411948.pro SAIS-YNSLMD-------DGEIAPSQNAS---VVRQHSRPRGNREDEVDVDLEELMVMEA 220 Ta_GI-408743661.pro CSTS-YSVPSY--QCTEQETECCSSEPSCSAQANMRSFHSRHTRDDNIDMNIEDMMVMEA 231 Hv_GI-164371454.pro CSTS-YSAPPY--RCTEQETECCSSEPSCSAQANMRSFHSRHTRDGNIDMNIEDMMVMEA 231 Bd_GI-357140854.pro CSTS-YSVPSY--QCTEQEAECCSSEPSCSAQSNMRPVHSRHNRDDNIGMNIEEMMVMEA 231 Os_GI-115445269.pro CSTS-FSVPSY--RCAEQETECCSSEPSCSAQTSMRPFHSRHNRDDNIDMNIEDMMVMEA 232 Sb_GI-242064618.pro CSTS-FSVPSY--QCTEQGNECCSSEPSCSSQANMRPFHSRHNRDDNVDVNLEDMMVMEA 233 Zm_GI-220961719.pro CSTS-FSVPSY--QRTEQGNECCSSEPSCSSQANMRPFHSRHNRDDNVDMNLEDMMVMET 235 Ta_GI-408743658.pro KTKEERSIEQFEEQKVIEAQMRVRQQALQDEEDKMKRKQSRCS--SSMDMNIEDMMVMEA 231 Bd_GI-357125256.pro GGTSTPAASSA------QGNDALLSQVQHSELLLKNSERLKQMRENNFDVDLEEVMLMEA 208 Os_GI-218197613.pro GGASTTVKSSG------QGSDMLSSQVQHAELLLKTSERLKQMRNNNFDMDPDEVMLVEA 227 Zm_GI-260935347.pro DGASTAVANSP------RGNDVLSSEVQHSELISRNSEAFKQMRGNNFEVDLEEVMLMEA 227 Sb_GI-242092026.pro DGASTGAASSP------QGSDAISSEVQHSELILRNSEAFKQMRGNNFDVDLEEVMLMEA 227    .                    .:                    .. :: :::*::*: Pt_GI-224061326.pro IWLSIQ-ENGRQKNPLCGDAAP-----PAQYTMEARYVTP----AMAPPLAGSSSSPSGG 268 Rc_GI-255578534.pro IWLSIQ-ENGRQKNPIYTDAAS-----SENYAVQGHYALQ----AMPP-VTESSSSPSGG 267 Vv_GI-147817790.pro IWLSIQ-DNGRHRNPLYGDTTT-----AEQYVTEEHYVLP----AMAP-QVESSSSPSGG 272 Gm_GI-356549538 pro IWLSIQ-ENGRRRNLSFVDATSGHYVADGRYVSSVSSVSS----VMGP-PTGSSSSPSGG 278 At_GI-18411948.pro IWLSVQ-ETGTQRNSASGEITS-----SRQYVTDNHSYVSSPPRVTPIVEPATPSSSSGG 274 Ta_GI-408743661.pro IWRSIQ-EQGSIGNPACGSFMP--------FEQP-TCERQ----AFVAAPPLEIPHP-GG 276 Hv_GI-164371454.pro IWRSIQ-EQGSIGNPACGSFMP--------FEQP-TRERQ----AFVAASPLEIPHP-GG 276 Bd_GI-357140854.pro IWRSIQ-EQGSMGNPVCGNFMP--------VIEPPSRERQ----AFVPAP-LEIPHP-GG 276 Os_GI-115445269.pro IWRSIQ---GSIGNPVCGNFMP--------VTEPSPRERQ----PFVPAASLEIPHG-GG 276 Sb_GI-242064618.pro IWRSIQ-EQGHLVNPVCGSYFP--------VIEPPSRERQ----AFLPAAPLEMPHP-GG 279 Zm_GI-220961719.pro IWRSIQQEQGHLVNPVCGSYFP--------VIEPPSRERQ----AFVPAAPLEMPHP-GG 282 Ta_GI-408743658.pro IWRSIQ-EQGSIGNPSCGSFMP--------FEQP-TRERQ----AFVAAPPLEMPHP-GG 276 Bd_GI-357125256.pro IWLSVQ-D--ASGNPGITGAAP--------PTIPPRSYD------TSVTASAEAAPSG-G 250 Os_GI-218197613.pro LWLSLQ-DQEASGNPTCGNTVS--------SVHPPRSFE------GSMTIPAEAASSSSA 272 Zm_GI-260935347.pro IWLSIQ-DQEALGNPGCVSTTP--------SSIPSRPFDD-----GDMTTTAEAASSG-G 272 Sb_GI-242092026.pro IWLSIQ-DQEALGNSGCVSTTP--------SSIPSRPFD------GAMTTTPEAASSG-G 271 :* *:*       *       .                                .    . Pt_GI-224061326.pro LACAIAALAERQQTGGES--IVHNSGNMPSFNMLPST-SSFYNRLEQDADNYSPAQSSSN 325 Rc_GI-255578534.pro LACAIAALAERQQTGGES--FAHNNENVAACNMLPGG-SSFYNRMDQDAENYSPAQGSNN 324 Vv_GI-147817790.pro LACAIAALAERQQMGGES--STNYNGNMPAFNMPPGS-SRFSNRVEQYPENYPPIESSMD 329 Gm_GI-356549538 pro LACAIAALAERQQMAGESS-MSLTNENMPSFNTLPGS-RRFYNRLGRDMANYPPGDNLNE 336 At_GI-18411948.pro LSCAISALAERQMVGESSSHNHNHNVNVSSYSMLPGN-CDSYYDIEQEVDGIDNHHHHR- 332 Ta_GI-408743661.pro FSCAVAAMAEHQ-PSSMDFSYMTGSSAFPVFDMFRRP-CNIAGGSMCAVE-SSPDSWSGI 333 Hv_GI-164371454.pro FSCAVAAMTEHQ-PSSMDFSYMTGSSAFPVFDMFRRP-CNIAGGSLRAVE-SSLDSWSGI 333 Bd_GI-357140854.pro FSCAVASMAEHQ-PPSMDFSYMAGNSAFPVFDMFRRQ-CNISGGSMCAVD-SSPDSWSGI 333 Os_GI-115445269.pro FSCAVAAMAEHQ-PPSMDFSYMAGSSAFPVFDMFRRP-CNIAGGSMCNLE-SSPESWSGI 333 Sb_GI-242064618.pro YSCAVAALAEHQ-PASMDFSYMAGSSTYPVFDMIRRP-CNMSSGSLCGVENSSLDTWSGI 337 Zm_GI-220961719.pro YSCAVAALAEHQ-APSMDFSYMSGSSTYPVFDMIRRP-CNMSSGSPCGAENSSLDTWSGI 340 Ta_GI-408743658.pro MDMNIEDMMVME-AIWRSIQEQ-GSIGNPSCGSFMPF-EQPTRERQAFVAAPPLEMPHPG 333 Bd_GI-357125256.pro FACAVAALAEQQHMLVGS--SIPATCQASKHDTLSRSDRSFTEDLSIAGSSSSGTRVDES 308 Os_GI-218197613.pro FACAVAALAEQQQMYGEA--SSTATCHTSRCDILSRSDRSFTEDLSINGSGSSGARSEEP 330 Zm_GI-260935347.pro FACAVAALAEQQHMHGES--SSASPCQTIRFGTLSRPDRSTTQDLSVAGSSSSDSRVEEP 330 Sb_GI-242092026.pro FAFAVAALAEQQHMHGES--SSASACQTPRFDILSRSDRSSTEDLSVVGSSSSDSRVEEP 329     :  :   :                   . Pt_GI-224061326.pro VLPDCRMIVTRDDGEWGADRGSDAAEAGTSYASSETAEDAGGISSLLPPP--PPTDEIGG 383 Rc_GI-255578534.pro MLSDCRMA--RDDVQWVADRGSDAAEAGTSYASSETTEDSDGISVVLPPPPLPPPDEIVG 382 Vv_GI-147817790.pro ALPDGGLAVTKDDGEWGVDRGSEVAEAGTSYASSDATDEAGGVAA------LPPTDEAEG Gm_GI-356549538 pro EPLDEAVTMTRSHGEWDMDHGTQLTETATSYTNSVAAEDRGELSS------LPRSDDNDG At_GI-18411948.pro -------------------HHYEMGETGSSNSYVSSYMTGEGFHN------FPPPP---- Ta_GI-408743661.pro ASSCSRREVVREEGECSTDHWSEGAEAGTSYAGSDIVVDAGTTPP------LPVTDN--- Hv_GI-164371454.pro APSGTRREMVREEGECSIDHWSEGAEAGTSYAGSDIMADAGTMPP------LPFADN--- Bd_GI-357140854.pro PPSCSR-EMIREEGECSTDHWSEGAEAGTSYAGSDIVADAGTMQQ------LPFAEN--- Os_GI-115445269.pro APSCSR-EVVREEGECSADHWSEGAEAGTSYAGSDIVADAGTMPQ------LPFAEN--- Sb_GI-242064618.pro APSCSR-EVVREEGECSTDHWSEGAEAGTSYAGSDIMADTGTMQP------LPFAEN--- Zm_GI-220961719.pro APSCSR-EVVRDEGECSADHWSEGAEAGTSYAGSDIMADAGAMQP------LPFAEN--- Ta_GI-408743658.pro GPSCSRREVVREEGECSTDHLSEGAEAGTSYAGSDIVVDAGTMLP------LPFADN--- Bd_GI-357125256.pro SINRTRQTREGAEHSNN-DRWSEVADASTSCAGSDITREAGAANL-------VASDG--- Os_GI-218197613.pro SSNKMHQTREGMEYSN--ERWSEMAEASSSFTGSDLTTEAGAAN----------SGG--- Zm_GI-260935347.pro PTSNTHRTIEAAEYSNSNVQWSEVAEAGTSIAESDGTVEAGVDNS-------STSAG--- Sb_GI-242092026.pro SSSSTHRTIEGSEYSNSNGRWSEVAEAGTSIAEADVIVEAGVGNS-------STSVG---                    :  :  ::.:* : Pt_GI-224061326.pro SFQNVSGPIP-ESFEEQMMLAMAVSLAEARAMTSG--PQSAWQ 423 Rc_GI-255578534.pro SS-DSGMIVP-ESFEEQMMLAMAVSLAEAQAMTGG--AGSAWG 420 Vv_GI-147817790.pro SFQNVGGPIVPESFEEQMMLAMAVSLAEARARTS---TQGVWQ 423 Gm_GI-356549538 pro SLQSATEPIVPESFEEQMMLAMAVSLAEARAMSSG--QSASWQ 431 At_GI-18411948.pro -----PLVIVPESFEEQMMMAMAVSMAEVHATTTCAPTEVTWQ 401 Ta_GI-408743661.pro -YSMVASHFRPESIEEQMMYSMAVSLAEA-HGRTHT-QGLAWL 424 Hv_GI-164371454.pro -YSMAASHFRPESIEEQMMYSMAVSLAEA-HGRTHT-QGLTWL 424 Bd_GI-357140854.pro -YNMAPSHFRPESIEEQMMYSMTVSLAEA-HGRTHS-QGLAWL 423 Os_GI-115445269.pro -FAMAPSHFRPESIEEQMMFSMALSLADG-BGRTRS-QGLAWL 423 Sb_GI-242064618.pro -FTMAPSHFRPESIEEQMMFSMAVSLAEAHHGRTQA-QGLAWL 428 Zm_GI-220961719.pro -FAMGPSHFRPESVEEQMMFSMAVSLAEAHHGRTQA-QGLAWL 431 Ta_GI-408743658.pro -YSMVASHFRPESIEEQMMYSMAVSLAEA-HGRTHS-QGLAWL 424 Bd_GI-357125256.pro --SSIGSGNIPDSFEDQMMLAISLSLVDARAMASSPGPGLTWQ 398 Os_GI-218197613.pro --SDTGAGSIPDSFEEQMMLAMALSLADARAKASSPG--LTWR 414 Zm_GI-260935347.pro --SNIDSVSVPDSFEEQMMLAMALSLVDARARAGSPG--LAWR 419 Sb_GI-242092026.pro --SNIGSSSVPDSFEEQMMLAMALSLVDARSRAGSPG--LAWR 418            :*.*:*** ::::*:.:             * * indicates identical residues : indicates conserved residues . indicates semi-conserved residues RING domain and first and second consensus domains are boxed.

TABLE 3 Alignment of DAI proteins (SEQ ID NOS: 41-64) Si_GI-514815267.pro ------------------------------------------------------------ Bd_GI-357157184.pro ------------------------------------------------------------ Br_DA1b.pro ------------------------------------------------------------ Br_DA1a.pro ------------------------------------------------------------ At_GI-15221983.pro ------------------------------------------------------------ Tc_GI-508722773.pro ------------------------------------------------------------ Gm_GI-356564241.pro ------------------------------------------------------------ Gm_GI-356552145.pro ------------------------------------------------------------ Vv_GI-302142429.pro ------------------------------------------------------------ Vv_GI-359492104.pro ------------------------------------------------------------ Sl_GI-460385048.pro ------------------------------------------------------------ Os_GI-218197709.pro ------------------------------------------------------------ Os_GI-115466772.pro ------------------------------------------------------------ Bd_GI-357160893.pro ------------------------------------------------------------ Bd_GI-357164660.pro ------------------------------------------------------------ Sb_GI-242092232.pro ------------------------------------------------------------ Zm_GI-212275448.pro ------------------------------------------------------------ At_GI-240256211.pro ------------------------------------------------------------ At GI-145360806.pro ------------------------------------------------------------ At_GI-22326876.pro MEPPAARVTPSIKADCSHSVNIICEETVLHSLVSHLSAALRREGISVFVDACGLQETKFF 60 At_GI-30698242.pro ------------------------------------------------------------ At_GI-30698240.pro ------------------------------------------------------------ At_GI-15240018.pro ------------------------------------------------------------ At_GI-334188680.pro ------------------------------------------------------------ Si_GI-514815267.pro ------------------------------------------------------------ Bd_GI-357157184.pro ------------------------------------------------------------ Br_DA1b.pro ------------------------------------------------------------ Br_DA1a.pro ------------------------------------------------------------ At_GI-15221983.pro ------------------------------------------------------------ Tc_GI-508722773.pro ------------------------------------------------------------ Gm_GI-356564241.pro ------------------------------------------------------------ Gm_GI-356552145.pro ------------------------------------------------------------ Vv_GI-302142429.pro ------------------------------------------------------------ Vv_GI-359492104.pro ------------------------------------------------------------ Sl_GI-460385048.pro ------------------------------------------------------------ Os_GI-218197709.pro ------------------------------------------------------------ Os_GI-115466772.pro ------------------------------------------------------------ Bd_GI-357160893.pro ------------------------------------------------------------ Bd_GI-357164660.pro ------------------------------------------------------------ Sb_GI-242092232.pro ------------------------------------------------------------ Zm_GI-212275448.pro ------------------------------------------------------------ At_GI-240256211.pro ------------------------------------------------------------ At GI-145360806.pro ------------------------------------------------------------ At_GI-22326876.pro SIKQNQPLTDGARVLVVVISDEVEFYDPWFPKFLKVIQGWQNNGHVVVPVFYGVDSLTRV 120 At_GI-30698242.pro ------------------------------------------------------------ At_GI-30698240.pro ------------------------------------------------------------ At_GI-15240018.pro ------------------------------------------------------------ At_GI-334188680.pro ------------------------------------------------------------ Si_GI-514815267.pro ------------------------------------------------------------ Bd_GI-357157184.pro ------------------------------------------------------------ Br_DA1b.pro ------------------------------------------------------------ Br_DA1a.pro ------------------------------------------------------------ At_GI-15221983.pro ------------------------------------------------------------ Tc_GI-508722773.pro ------------------------------------------------------------ Gm_GI-356564241.pro ------------------------------------------------------------ Gm_GI-356552145.pro ------------------------------------------------------------ Vv_GI-302142429.pro ------------------------------------------------------------ Vv_GI-359492104.pro ------------------------------------------------------------ Sl_GI-460385048.pro ------------------------------------------------------------ Os_GI-218197709.pro ------------------------------------------------------------ Os_GI-115466772.pro ------------------------------------------------------------ Bd_GI-357160893.pro ------------------------------------------------------------ Bd_GI-357164660.pro ------------------------------------------------------------ Sb_GI-242092232.pro ------------------------------------------------------------ Zm_GI-212275448.pro ------------------------------------------------------------ At_GI-240256211.pro ------------------------------------------------------------ At GI-145360806.pro ------------------------------------------------------------ At_GI-22326876.pro YGWANSWLEAEKLTSHQSKILSNNVLTDSELVEEIVRDVYGKLYPAERVGIYARLLEIEK 180 At_GI-30698242.pro ------------------------------------------------------------ At_GI-30698240.pro ------------------------------------------------------------ At_GI-15240018.pro ------------------------------------------------------------ At_GI-334188680.pro ------------------------------------------------------------ Si_GI-514815267.pro ------------------------------------------------------------ Bd_GI-357157184.pro ------------------------------------------------------------ Br_DA1b.pro ------------------------------------------------------------ Br_DA1a.pro ------------------------------------------------------------ At_GI-15221983.pro ------------------------------------------------------------ Tc_GI-508722773.pro ------------------------------------------------------------ Gm_GI-356564241.pro ------------------------------------------------------------ Gm_GI-356552145.pro ------------------------------------------------------------ Vv_GI-302142429.pro ------------------------------------------------------------ Vv_GI-359492104.pro ------------------------------------------------------------ Sl_GI-460385048.pro ------------------------------------------------------------ Os_GI-218197709.pro ------------------------------------------------------------ Os_GI-115466772.pro ------------------------------------------------------------ Bd_GI-357160893.pro ------------------------------------------------------------ Bd_GI-357164660.pro ------------------------------------------------------------ Sb_GI-242092232.pro ------------------------------------------------------------ Zm_GI-212275448.pro ------------------------------------------------------------ At_GI-240256211.pro ------------------------------------------------------------ At GI-145360806.pro ------------------------------------------------------------ At_GI-22326876.pro LLYKQHRDIRSIGIWGMPGIGKTTLAKAVFNHMSTDYDASCFIENFDEAFHKEGLHRLLK 240 At_GI-30698242.pro ------------------------------------------------------------ At_GI-30698240.pro ------------------------------------------------------------ At_GI-15240018.pro ------------------------------------------------------------ At_GI-334188680.pro ------------------------------------------------------------ Si_GI-514815267.pro ------------------------------------------------------------ Bd_GI-357157184.pro ------------------------------------------------------------ Br_DA1b.pro ------------------------------------------------------------ Br_DA1a.pro ------------------------------------------------------------ At_GI-15221983.pro ------------------------------------------------------------ Tc_GI-508722773.pro ------------------------------------------------------------ Gm_GI-356564241.pro ------------------------------------------------------------ Gm_GI-356552145.pro ------------------------------------------------------------ Vv_GI-302142429.pro ------------------------------------------------------------ Vv_GI-359492104.pro ------------------------------------------------------------ Sl_GI-460385048.pro ------------------------------------------------------------ Os_GI-218197709.pro ------------------------------------------------------------ Os_GI-115466772.pro ------------------------------------------------------------ Bd_GI-357160893.pro ------------------------------------------------------------ Bd_GI-357164660.pro ------------------------------------------------------------ Sb_GI-242092232.pro ------------------------------------------------------------ Zm_GI-212275448.pro ------------------------------------------------------------ At_GI-240256211.pro ------------------------------------------------------------ At GI-145360806.pro ------------------------------------------------------------ At_GI-22326876.pro ERIGKILKDEFDIESSYIMRPTLHRDKLYDKRILVVLDDVRDSLAAESFLKRLDWFGSGS 300 At_GI-30698242.pro ------------------------------------------------------------ At_GI-30698240.pro ------------------------------------------------------------ At_GI-15240018.pro ------------------------------------------------------------ At_GI-334188680.pro ------------------------------------------------------------ Si_GI-514815267.pro ------------------------------------------------------------ Bd_GI-357157184.pro ------------------------------------------------------------ Br_DA1b.pro ------------------------------------------------------------ Br_DA1a.pro ------------------------------------------------------------ At_GI-15221983.pro ------------------------------------------------------------ Tc_GI-508722773.pro ------------------------------------------------------------ Gm_GI-356564241.pro ------------------------------------------------------------ Gm_GI-356552145.pro ------------------------------------------------------------ Vv_GI-302142429.pro ------------------------------------------------------------ Vv_GI-359492104.pro ------------------------------------------------------------ Sl_GI-460385048.pro ------------------------------------------------------------ Os_GI-218197709.pro ------------------------------------------------------------ Os_GI-115466772.pro ------------------------------------------------------------ Bd_GI-357160893.pro ------------------------------------------------------------ Bd_GI-357164660.pro ------------------------------------------------------------ Sb_GI-242092232.pro ------------------------------------------------------------ Zm_GI-212275448.pro ------------------------------------------------------------ At_GI-240256211.pro ------------------------------------------------------------ At GI-145360806.pro ------------------------------------------------------------ At_GI-22326876.pro LIIITSVDKQVFAFCQINQIYTVQGLNVHEALQLFSQSVFGINEPEQNDRKLSMKVIDYV 360 At_GI-30698242.pro ------------------------------------------------------------ At_GI-30698240.pro ------------------------------------------------------------ At_GI-15240018.pro ------------------------------------------------------------ At_GI-334188680.pro ------------------------------------------------------------ Si_GI-514815267.pro ------------------------------------------------------------ Bd_GI-357157184.pro ------------------------------------------------------------ Br_DA1b.pro ------------------------------------------------------------ Br_DA1a.pro ------------------------------------------------------------ At_GI-15221983.pro ------------------------------------------------------------ Tc_GI-508722773.pro ------------------------------------------------------------ Gm_GI-356564241.pro ------------------------------------------------------------ Gm_GI-356552145.pro ------------------------------------------------------------ Vv_GI-302142429.pro ------------------------------------------------------------ Vv_GI-359492104.pro ------------------------------------------------------------ Sl_GI-460385048.pro ------------------------------------------------------------ Os_GI-218197709.pro ------------------------------------------------------------ Os_GI-115466772.pro ------------------------------------------------------------ Bd_GI-357160893.pro ------------------------------------------------------------ Bd_GI-357164660.pro ------------------------------------------------------------ Sb_GI-242092232.pro ------------------------------------------------------------ Zm_GI-212275448.pro ------------------------------------------------------------ At_GI-240256211.pro ------------------------------------------------------------ At GI-145360806.pro ------------------------------------------------------------ At_GI-22326876.pro NGNPLALSIYGRELMGKKSEMETAFFELKHCPPLKIQDVLKNAYSALSDNEKNIVLDIAF 420 At_GI-30698242.pro ------------------------------------------------------------ At_GI-30698240.pro ------------------------------------------------------------ At_GI-15240018.pro ------------------------------------------------------------ At_GI-334188680.pro ------------------------------------------------------------ Si_GI-514815267.pro ------------------------------------------------------------ Bd_GI-357157184.pro ------------------------------------------------------------ Br_DA1b.pro ------------------------------------------------------------ Br_DA1a.pro ------------------------------------------------------------ At_GI-15221983.pro ------------------------------------------------------------ Tc_GI-508722773.pro ------------------------------------------------------------ Gm_GI-356564241.pro ------------------------------------------------------------ Gm_GI-356552145.pro ------------------------------------------------------------ Vv_GI-302142429.pro ------------------------------------------------------------ Vv_GI-359492104.pro ------------------------------------------------------------ Sl_GI-460385048.pro ------------------------------------------------------------ Os_GI-218197709.pro ------------------------------------------------------------ Os_GI-115466772.pro ------------------------------------------------------------ Bd_GI-357160893.pro ------------------------------------------------------------ Bd_GI-357164660.pro ------------------------------------------------------------ Sb_GI-242092232.pro ------------------------------------------------------------ Zm_GI-212275448.pro ------------------------------------------------------------ At_GI-240256211.pro ------------------------------------------------------------ At GI-145360806.pro ------------------------------------------------------------ At_GI-22326876.pro FFKGETVNYVMQLLEESHYFPRLAIDVLVDKCVLTISENTVQMNNLIQDTCQEIFNGEIE 480 At_GI-30698242.pro ------------------------------------------------------------ At_GI-30698240.pro ------------------------------------------------------------ At_GI-15240018.pro ------------------------------------------------------------ At_GI-334188680.pro ------------------------------------------------------------ Si_GI-514815267.pro ------------------------------------------------------------ Bd_GI-357157184.pro ------------------------------------------------------------ Br_DA1b.pro ------------------------------------------------------------ Br_DA1a.pro ------------------------------------------------------------ At_GI-15221983.pro ------------------------------------------------------------ Tc_GI-508722773.pro ------------------------------------------------------------ Gm_GI-356564241.pro ------------------------------------------------------------ Gm_GI-356552145.pro ------------------------------------------------------------ Vv_GI-302142429.pro ------------------------------------------------------------ Vv_GI-359492104.pro ------------------------------------------------------------ Sl_GI-460385048.pro ------------------------------------------------------------ Os_GI-218197709.pro ------------------------------------------------------------ Os_GI-115466772.pro ------------------------------------------------------------ Bd_GI-357160893.pro ------------------------------------------------------------ Bd_GI-357164660.pro ------------------------------------------------------------ Sb_GI-242092232.pro ------------------------------------------------------------ Zm_GI-212275448.pro ------------------------------------------------------------ At_GI-240256211.pro ------------------------------------------------------------ At GI-145360806.pro ------------------------------------------------------------ At_GI-22326876.pro TCTRMWEPSRIRYLLEYDELEGSGETKAMPKSGLVAEHIESIFLDTSNVKFDVKHDAFKN 540 At_GI-30698242.pro ------------------------------------------------------------ At_GI-30698240.pro ------------------------------------------------------------ At_GI-15240018.pro ------------------------------------------------------------ At_GI-334188680.pro ------------------------------------------------------------ Si_GI-514815267.pro ------------------------------------------------------------ Bd_GI-357157184.pro ------------------------------------------------------------ Br_DA1b.pro ------------------------------------------------------------ Br_DA1a.pro ------------------------------------------------------------ At_GI-15221983.pro ------------------------------------------------------------ Tc_GI-508722773.pro ------------------------------------------------------------ Gm_GI-356564241.pro ------------------------------------------------------------ Gm_GI-356552145.pro ------------------------------------------------------------ Vv_GI-302142429.pro ------------------------------------------------------------ Vv_GI-359492104.pro ------------------------------------------------------------ Sl_GI-460385048.pro ------------------------------------------------------------ Os_GI-218197709.pro ------------------------------------------------------------ Os_GI-115466772.pro ------------------------------------------------------------ Bd_GI-357160893.pro ------------------------------------------------------------ Bd_GI-357164660.pro ------------------------------------------------------------ Sb_GI-242092232.pro ------------------------------------------------------------ Zm_GI-212275448.pro ------------------------------------------------------------ At_GI-240256211.pro ------------------------------------------------------------ At GI-145360806.pro ------------------------------------------------------------ At_GI-22326876.pro MFNLKFLKIYNSCSKYISGLNFPKGLDSLPYELRLLHWENYPLQSLPQDFDFGHLVKLSM 600 At_GI-30698242.pro ------------------------------------------------------------ At_GI-30698240.pro ------------------------------------------------------------ At_GI-15240018.pro ------------------------------------------------------------ At_GI-334188680.pro ------------------------------------------------------------ Si_GI-514815267.pro ------------------------------------------------------------ Bd_GI-357157184.pro ------------------------------------------------------------ Br_DA1b.pro ------------------------------------------------------------ Br_DA1a.pro ------------------------------------------------------------ At_GI-15221983.pro ------------------------------------------------------------ Tc_GI-508722773.pro ------------------------------------------------------------ Gm_GI-356564241.pro ------------------------------------------------------------ Gm_GI-356552145.pro ------------------------------------------------------------ Vv_GI-302142429.pro ------------------------------------------------------------ Vv_GI-359492104.pro ------------------------------------------------------------ Sl_GI-460385048.pro ------------------------------------------------------------ Os_GI-218197709.pro ------------------------------------------------------------ Os_GI-115466772.pro ------------------------------------------------------------ Bd_GI-357160893.pro ------------------------------------------------------------ Bd_GI-357164660.pro ------------------------------------------------------------ Sb_GI-242092232.pro ------------------------------------------------------------ Zm_GI-212275448.pro ------------------------------------------------------------ At_GI-240256211.pro ------------------------------------------------------------ At GI-145360806.pro ------------------------------------------------------------ At_GI-22326876.pro PYSQLHKLGTRVKDLVMLKRLILSHSLQLVECDILIYAQNIELIDLQGCTGLQRFPDTSQ 660 At_GI-30698242.pro ------------------------------------------------------------ At_GI-30698240.pro ------------------------------------------------------------ At_GI-15240018.pro ------------------------------------------------------------ At_GI-334188680.pro ------------------------------------------------------------ Si_GI-514815267.pro ------------------------------------------------------------ Bd_GI-357157184.pro ------------------------------------------------------------ Br_DA1b.pro ------------------------------------------------------------ Br_DA1a.pro ------------------------------------------------------------ At_GI-15221983.pro ------------------------------------------------------------ Tc_GI-508722773.pro ------------------------------------------------------------ Gm_GI-356564241.pro ------------------------------------------------------------ Gm_GI-356552145.pro ------------------------------------------------------------ Vv_GI-302142429.pro ------------------------------------------------------------ Vv_GI-359492104.pro ------------------------------------------------------------ Sl_GI-460385048.pro ------------------------------------------------------------ Os_GI-218197709.pro ------------------------------------------------------------ Os_GI-115466772.pro -------------------------------------------------------MGDRP 5 Bd_GI-357160893.pro ------------------------------------------------------------ Bd_GI-357164660.pro ------------------------------------------------------------ Sb_GI-242092232.pro ------------------------------------------------------------ Zm_GI-212275448.pro ------------------------------------------------------------ At_GI-240256211.pro ------------------------------------------------------------ At GI-145360806.pro ------------------------------------------------------------ At_GI-22326876.pro LQNLRVVNLSGCTEIKCFSGVPPNIEELHLQGTRIREIPIFNATHPPKVKLDRKKLWNLL 720 At_GI-30698242.pro ------------------------------------------------------------ At_GI-30698240.pro ------------------------------------------------------------ At_GI-15240018.pro ------------------------------------------------------------ At_GI-334188680.pro ------------------------------------------------------------ Si_GI-514815267.pro ------------------------------------------------------------ Bd_GI-357157184.pro ------------------------------------------------------------ Br_DA1b.pro ------------------------------------------------------------ Br_DA1a.pro ------------------------------------------------------------ At_GI-15221983.pro ------------------------------------------------------------ Tc_GI-508722773.pro ------------------------------------------------------------ Gm_GI-356564241.pro ------------------------------------------------------------ Gm_GI-356552145.pro ------------------------------------------------------------ Vv_GI-302142429.pro ------------------------------------------------------------ Vv_GI-359492104.pro ------------------------------------------------------------ Sl_GI-460385048.pro ------------------------------------------------------------ Os_GI-218197709.pro DMGAGVALRFSHNDWTLEEDSKALHFLQPDLVLFTGDYGNENVQLVKSISDLQLPKAAIL 65 Os_GI-115466772.pro ------------------------------------------------------------ Bd_GI-357160893.pro ------------------------------------------------------------ Bd_GI-357164660.pro ------------------------------------------------------------ Sb_GI-242092232.pro ------------------------------------------------------------ Zm_GI-212275448.pro ------------------------------------------------------------ At_GI-240256211.pro ------------------------------------------------------------ At GI-145360806.pro ------------------------------------------------------------ At_GI-22326876.pro ENFSDVEHIDLECVTNLATVTSNNHVMGKLVCLNMKYCSNLRGLPDMVSLESLKVLYLSG 780 At_GI-30698242.pro ------------------------------------------------------------ At_GI-30698240.pro ------------------------------------------------------------ At_GI-15240018.pro ------------------------------------------------------------ At_GI-334188680.pro ------------------------------------------------------------ Si_GI-514815267.pro ------------------------------------------------------------ Bd_GI-357157184.pro ------------------------------------------------------------ Br_DA1b.pro ------------------------------------------------------------ Br_DA1a.pro ------------------------------------------------------------ At_GI-15221983.pro ------------------------------------------------------------ Tc_GI-508722773.pro ------------------------------------------------------------ Gm_GI-356564241.pro ------------------------------------------------------------ Gm_GI-356552145.pro ------------------------------------------------------------ Vv_GI-302142429.pro ------------------------------------------------------------ Vv_GI-359492104.pro ------------------------------------------------------------ Sl_GI-460385048.pro ------------------------------------------------------------ Os_GI-218197709.pro GNHDCWHTYQFSEKKVDRVQLQLESLGEQHVGYKCLDFPTIKLSVVGGRPFSCGGNRIFR 125 Os_GI-115466772.pro ------------------------------------------------------------ Bd_GI-357160893.pro ------------------------------------------------------------ Bd_GI-357164660.pro ------------------------------------------------------------ Sb_GI-242092232.pro ------------------------------------------------------------ Zm_GI-212275448.pro ------------------------------------------------------------ At_GI-240256211.pro ------------------------------------------------------------ At GI-145360806.pro ------------------------------------------------------------ At_GI-22326876.pro CSELEKIMGFPRNLKKLYVGGTAIRELPQLPNSLEFLNAHGCKHLKSINLDFEQLPRHFI 840 At_GI-30698242.pro ------------------------------------------------------------ At_GI-30698240.pro ------------------------------------------------------------ At_GI-15240018.pro ------------------------------------------------------------ At_GI-334188680.pro ------------------------------------------------------------ Si_GI-514815267.pro ------------------------------------------------------------ Bd_GI-357157184.pro ------------------------------------------------------------ Br_DA1b.pro ------------------------------------------------------------ Br_DA1a.pro ------------------------------------------------------------ At_GI-15221983.pro ------------------------------------------------------------ Tc_GI-508722773.pro ------------------------------------------------------------ Gm_GI-356564241.pro ------------------------------------------------------------ Gm_GI-356552145.pro ------------------------------------------------------------ Vv_GI-302142429.pro ------------------------------------------------------------ Vv_GI-359492104.pro ------------------------------------------------------------ Sl_GI-460385048.pro ------------------------------------------------------------ Os_GI-218197709.pro ------------------------------------------------------------ Os_GI-115466772.pro PKLLSKWYGVNDMAESAKRIYDAATNAPKEHAVILLAHNGPTGLGSRMEDICGRDWVAGG 185 Bd_GI-357160893.pro ------------------------------------------------------------ Bd_GI-357164660.pro ------------------------------------------------------------ Sb_GI-242092232.pro ------------------------------------------------------------ Zm_GI-212275448.pro ------------------------------------------------------------ At_GI-240256211.pro ------------------------------------------------------------ At GI-145360806.pro ------------------------------------------------------------ At_GI-22326876.pro FSNCYRFSSQVIAEFVEKGLVASLARAKQEELIKAPEVIICIPMDTRQRSSFRLQAGRNA 900 At_GI-30698242.pro ------------------------------------------------------------ At_GI-30698240.pro ---------------------------------------MPISDVASLVGGAALGAPLSE 21 At_GI-15240018.pro ---------------------------------------MASDYYSSDDEGFGEKVGLIG 21 At_GI-334188680.pro ---------------------------------------------MWCLSCFKPSTKHDP 15 Si_GI-514815267.pro ------------------------------------------------------------ Bd_GI-357157184.pro ------------------------------------------------------------ Br_DA1b.pro ------------------------------------------------------------ Br_DA1a.pro ------------------------------------------------------------ At_GI-15221983.pro ------------------------------------------------------------ Tc_GI-508722773.pro ------------------------------------------------------------ Gm_GI-356564241.pro ------------------------------------------------------------ Gm_GI-356552145.pro ------------------------------------------------------------ Vv_GI-302142429.pro ------------------------------------------------------------ Vv_GI-359492104.pro ------------------------------------------------------------ Sl_GI-460385048.pro ------------------------------------------------------------ Os_GI-218197709.pro ------------------------------------------------------------ Os_GI-115466772.pro ------------------------------------------------------------ Bd_GI-357160893.pro GDHGDPDLEQAISDLQRETGVSIPLVVFGHMHKSLAYGRGLRKMIAFGANRTIYLNGAVV 245 Bd_GI-357164660.pro ------------------------------------------------------------ Sb_GI-242092232.pro ------------------------------------------------------------ Zm_GI-212275448.pro ------------------------------------------------------------ At_GI-240256211.pro ------------------------------------------------------------ At GI-145360806.pro ------------------------------------------------------------ At_GI-22326876.pro MTDLVPWMQKPISGFSMSVVVSFQDDYHNDVGLRIRCVGTWKTWNNQPDRIVERFFQCWA 960 At_GI-30698242.pro ------------------------------------------------------------ At_GI-30698240.pro IFKLVIEEAKKVKDFKP------------------------------------------L 39 At_GI-15240018.pro EKDRFEAETIHVIEVSQ------------------------------------------H 39 At_GI-334188680.pro SEDRFEEETNIVTGIS-------------------------------------------- 31 Si_GI-514815267.pro ------------------------------------------------------------ Bd_GI-357157184.pro ------------------------------------------------------------ Br_DA1b.pro ------------------------------------------------------------ Br_DA1a.pro ------------------------------------------------------------ At_GI-15221983.pro ------------------------------------------------------------ Tc_GI-508722773.pro ------------------------------------------------------------ Gm_GI-356564241.pro ------------------------------------------------------------ Gm_GI-356552145.pro ------------------------------------------------------------ Vv_GI-302142429.pro ------------------------------------------------------------ Vv_GI-359492104.pro ------------------------------------------------------------ Sl_GI-460385048.pro ------------------------------------------------------------ Os_GI-218197709.pro PRVNHAQSSRQPAISTSEKTGLEGLTGLMVPTSRAFTIVDLFEGAVEKISEVWVTVGDAR 305 Os_GI-115466772.pro ------------------------------------------------------------ Bd_GI-357160893.pro ------------------------------------------------------------ Bd_GI-357164660.pro ------------------------------------------------------------ Sb_GI-242092232.pro ------------------------------------------------------------ Zm_GI-212275448.pro ------------------------------------------------------------ At_GI-240256211.pro ------------------------------------------------------------ At GI-145360806.pro --------------------------------------MDSSSSSSSSSPSSSYGVARVS 22 At_GI-22326876.pro PTEAPKVVADHIFVLYDTKMHPSDSEENHISMWAHEVKFEFHTVSGENNPLGASCKVTEC 1020 At_GI-30698242.pro ------------------------------------------------------------ At_GI-30698240.pro SQDLASTMERLVPIFNEIDMMQQGSNRGTSELKVLTETMERAGEMVHKCSRIQWYSIAKK 99 At_GI-15240018.pro EADIQKAKQRSLATHEAEKLDLATHEAEQLDLAIQEFSRQEEEEERRRTRELENDAQIAN 99 At_GI-334188680.pro -------------LYEDVILRQRRSEADQIEWAIQDSFNPQE---TSRCRQREEDDQIAR 75 Si_GI-514815267.pro --------------------------MGWLSKIFKGSVN-RVSRGHYNGNSHE----GYS 29 Bd_GI-357157184.pro --------------------------MGWLNKIFKGSVN-RVSRGNYDGNWHD----GNS 29 Br_DA1b.pro --------------------------MGWLNKIFKGSNQ-RHPLGNEHYHHNGGYYENYP 33 Br_DA1a.pro --------------------------MGWFNKIFKGSTQ-RFRLGNDHDHN--GYYQSYP 31 At_GI-15221983.pro --------------------------MGWFNKIFKGSNQ-RLRVGNNKHNHN-VYYDNYP 32 Tc_GI-508722773.pro --------------------------MDWIKKIFKGCAH-KFSEG---HHHG-----NYV 25 Gm_GI-356564241.pro --------------------------MGWLSRIFKGSDHNKLSEGHYYKEDA-----GYY 29 Gm_GI-356552145.pro --------------------------MGWLSRIFKGSDHNKLSEGHYYKEDA-----GYY 29 Vv_GI-302142429.pro --------------------------MGWLNKIFKGSSH-KISEGNYHGRYQ-----GDT 28 Vv_GI-359492104.pro --------------------------MGWLNKIFKGSSH-KISEGNYHGRYQ-----GDT 28 Sl_GI-460385048.pro --------------------------MGWLNKIFRGSSH-KISEGQYDWRCE-----GHT 28 Os_GI-218197709.pro TELEQELVLYKQPHKSVPSNIAIWSTMGWLTKFFRGSTH-KISEGQYHSKPAEETIWNGP 364 Os_GI-115466772.pro --------------------------MGWLTKFFRGSTH-KISEGQYHSKPAEETIWNGP 33 Bd_GI-357160893.pro --------------------------MGWLTKIFRGSTY-KISEGQRQSRPAEEAVWNEP 33 Bd_GI-357164660.pro --------------------------MGWLTKFFRGSTH-NISEGQDQSKPAEETVWNEP 33 Sb_GI-242092232.pro --------------------------MGWLTKFFRGSTH-NISEGQYHSRPAEDTAWNEP 33 Zm_GI-212275448.pro --------------------------MGWLTKFFRGSTH-NISEEQYHSRPAEDTAWNEP 33 At_GI-240256211.pro --------------------------MGWLTKILKGSSH-KFSDGQCNGRYREDRNLEGP 33 At GI-145360806.pro HISNPCIFGEVGSSSSSTYRDKKWKLMKWVSKLFKSGSNGGGSGAHTNHHPPQFQEDENM 82 At_GI-22326876.pro GVEVITAATGDTSVSGIIRESETITIIEKEDTIIDEEDTPLLSRKPEETNRSRSSSELQK 1080 At_GI-30698242.pro ------------------------------------------------------------ At_GI-30698240.pro ALYTREIKA--INQDFLKFCQIELQLIQHRNQLQYMRSMGMASVSTKADLLSDIGNEFSK 157 At_GI-15240018.pro VLQHEERE---------RLINKKTALEDEEDELLARTLEESLKENNRRKMFEEQVNKDEQ 150 At_GI-334188680.pro GLQYVEET------------ELDKSVVDEED---------------------------QQ 96 Si_GI-514815267.pro TQHTKSY----------------------------------------------------- 36 Bd_GI-357157184.pro SENIR------------------------------------------------------- 34 Br_DA1b.pro -HEHS------EPSAETDA--------------------------------------DHT 48 Br_DA1a.pro -HDEPSADTDPDPDPDPDE--------------------------------------THT 52 At_GI-15221983.pro TASHDDEPSAADTDADNDEP-------------------------------------HHT 55 Tc_GI-508722773.pro EDPHP-----------------------------------------------------QF 32 Gm_GI-356564241.pro LPSTS------------------------------------------------------- 34 Gm_GI-356552145.pro LPSTS------------------------------------------------------- 34 Vv_GI-302142429.pro VQNEP------------------------------------------------------- 33 Vv_GI-359492104.pro VQNEP------------------------------------------------------- 33 Sl_GI-460385048.pro EEDDP------------------------------------------------------- 33 Os_GI-218197709.pro SNSAVVTMVYPLESTFGQLDLLLLATDLRQLVIDDVDCCKLRQQAQPVLHLMYSQLQLLQ 424 Os_GI-115466772.pro SNSAVVT----------------------------------------------------- 40 Bd_GI-357160893.pro SSSTVVT----------------------------------------------------- 40 Bd_GI-357164660.pro SSSTAVN----------------------------------------------------- 40 Sb_GI-242092232.pro SSSPVVT----------------------------------------------------- 40 Zm_GI-212275448.pro SSSPVVT----------------------------------------------------- 40 At_GI-240256211.pro RYSAEGSDFDKEEIECAIALSLS--------------------EQEHVIPQDDKGKKIIE 73 At GI-145360806.pro VFPLPPS----------------------------------------------------- 89 At_GI-22326876.pro LSSTSSKVRSKGNVFWKWLGCFP------------------LQPKNLRSRSRRTTALEEA 1122 At_GI-30698242.pro ------------------------------------------------------------ At_GI-30698240.pro LCLVAQPEVVTKFWLKRPLMELKKMLFEDGV----------VTVVVSAPYALGKTTLVTK 207 At_GI-15240018.pro LALIVQESLNMEEYPIR-LEEYK-------------------SISRRAPLDVDEQ-FAKA 189 At_GI-334188680.pro LSKIVEESLKE------------------------------------------------- 107 Si_GI-514815267.pro --------GAHGNED-E-----------DMDHAIALSLSEQDQRKGKAIDTEHHLD--ED 74 Bd_GI-357157184.pro --------GAYDESDNE-----------DIDRAIALSLAEEDPNKGKAIIDPDYS----- 70 Br_DA1b.pro QEPSTSEEETWNGKENE-----------EVDRVIALSILEE-ENQRPETNTG-------- 88 Br_DA1a.pro QEPSTSEEDTS-GQENE-----------DIDRAIALSLIENSQGQTNNTCAAN------- 93 At_GI-15221983.pro QEPSTSEDNTSNDQENE-----------DIDRAIALSLLEE--NQEQTSISG-------- 94 Tc_GI-508722773.pro NAPSVS-GDAWQELENE-----------DVDRAIALSLLGE--SQKGRKVID-------- 70 Gm_GI-356564241.pro GVTN-------NQNENE-----------DIDRAIALSLVEESRRANNNVNGER------- 69 Gm_GI-356552145.pro GVTNDAWNQSQNQNENE-----------DIDRAIALSLVEETQKANNNVN---------- 73 Vv_GI-302142429.pro ----SCSGDVWAETENE-----------DIDRAIALSLSEE--EQKGKKVID-------- 68 Vv_GI-359492104.pro ----SCSGDVWAETENE-----------DIDRAIALSLSEE--EQKGKKVIDE------- 69 Sl_GI-460385048.pro ----STAEDSWSEIE-------------EIDRAIAISLSEE--EQKGKIVID-------- 66 Os_GI-218197709.pro TSHAHQHGDVPSEFDNE-----------DIARAISLSLLEEEQRKAKAIEKD-------- 465 Os_GI-115466772.pro --------DVPSEFDNE-----------DIARAISLSLLEEEQRKAKAIEKD-------- 73 Bd_GI-357160893.pro --------DVLSEFDNE-----------DIDRAIALSLSEE-QRKSKGTGKD-------- 72 Bd_GI-357164660.pro --------YALSEFDNE-----------DIDRAIALSLSEEEQRKSKGTGKD-------- 73 Sb_GI-242092232.pro --------DIFSEFNNE-----------DIDRAIALSLSEEEQRKAKTIDKD-------- 73 Zm_GI-212275448.pro --------DILSEFNNE-----------DIDRAIALSLSEEEQRKEKAIDKD-------- 73 At_GI-240256211.pro YKSETEEDDDDDEDEDEEYMRAQLEAAEEEERRVAQAQIEEEEKRRAEAQLEETEKLLAK 133 At GI-145360806.pro ----SLDDRSRGARDKE-----------ELDRSISLSLADN-TKRPHGYGWS-------- 125 At_GI-22326876.pro LEEALKEREKLEDTREL-----------QIALIESKKIKKIKQADERDQIKHADER---- 1167 At_GI-30698242.pro ----MVRRKRQEEDEKI-----------EIERVKEESLKLAKQAEEKRRLEESKEQ---- 41 At_GI-30698240.pro LCHDADVKEKFKQIFFI-----------SVSKFPNVRLIGHKLLEHIGCKANEYEN---- 252 At_GI-15240018.pro VKESLKNKGKGKQFEDE-----------QVKKDEQLALIVQESLNMVESPPRLEEN---- 234 At_GI-334188680.pro -------KGKSKQFEDD-----------QVENDEQQALMVQESLYMVELSAQLEED---- 145 Si_GI-514815267.pro EQLARALQENTSPTLDEDEQLAR--------------------------ALQESMNDEHP 108 Bd_GI-357157184.pro --------------LEEDEQLAR--------------------------ALHESLNTGSP 90 Br_DA1b.pro -------AWKHAM-MDDDEQLAR--------------------------AIQESMIARN- 113 Br_DA1a.pro -------AGKYAM-VDEDEQLAR--------------------------AIQESMVVGNT 119 At_GI-15221983.pro ---------KYSMPVDEDEQLAR--------------------------ALQESMVVGNS 119 Tc_GI-508722773.pro ----------DEYQLEEDEQLAR--------------------------ALQESLNFEPP 94 Gm_GI-356564241.pro -------ILSLQTLLEEDEQLAR--------------------------AIEQSLNLESP 96 Gm_GI-356552145.pro ---------DYRSQLEEDEQLAR--------------------------AIEQSLNLESP 98 Vv_GI-302142429.pro ----------NEFQLEEDEQLAR--------------------------AIQESLNIESP 92 Vv_GI-359492104.pro -------L-DNEFQLEEDEQLAR--------------------------AIQESLNIESP 95 Sl_GI-460385048.pro ----------SESQLKEDEQLAR--------------------------ALQESLNVESP 90 Os_GI-218197709.pro ------------MHLEEDEQLAR--------------------------AIQESLNVESP 487 Os_GI-115466772.pro ------------MHLEEDEQLAR--------------------------AIQESLNVESP 95 Bd_GI-357160893.pro ------------LHLDEDEQLAR--------------------------AIHESLNVESP 94 Bd_GI-357164660.pro ------------QHLDEDEQLAR--------------------------AIQESLNVESP 95 Sb_GI-242092232.pro ------------MHLEEDEQLAR--------------------------AIQESLNVESP 95 Zm_GI-212275448.pro ------------MHLEEDEQLAR--------------------------AIQESLNVESP 95 At_GI-240256211.pro ARLEEEEMRRSKAQLEEDELLAK--------------------------ALQESMNVGSP 167 At GI-145360806.pro --------------MDNNRDFPR--------------------------PFHGGLNPSSF 145 At_GI-22326876.pro ------EQRKHSKDHEEEEIESNEKEERRHSKDYVIEELVLKGKGKRKQLDDDKADEKEQ 1221 At_GI-30698242.pro ------GKRIQVDDD---------------------------------QLAKTTSKDKGQ 62 At_GI-30698240.pro ------DLDAMLYIQQLLKQLGRNGSILLVLDDV--------------WAEEESLLQKFL 292 At_GI-15240018.pro ------NNISTRAPVDEDEQLAK--------------------------AVEESLKGKGQ 262 At_GI-334188680.pro ------KNISTIPPLNEDAQLQK--------------------------VIWESAKGKGQ 173 Si_GI-514815267.pro PR--------------------------QHIPIEDVHSESAPASSLPPYVFPTNGSRVCA 142 Bd_GI-357157184.pro PH -------------------------QNVPVVDVPSERVPTPEPPPPVPLSSGPPACA 124 Br_DA1b.pro -----GTT------YDFGNAY------GNGHMHGGGNVYDNGDIYYPRPIAFSMDFRICA 156 Br_DA1a.pro PRQKHGSS------YDIGNAYGAGDVYGNGHHHGGGNVYANGDIYYPRPTAFPMDFRICA 173 At_GI-15221983.pro PRHKSGST------YDNGNAYGAGDLYGNGHMYGGGNVYANGDIYYPRPITFQMDFRICA 173 Tc_GI-508722773.pro P------------------------------------QYENANMYQPMPVHFPMGYRICA 118 Gm_GI-356564241.pro P------------------------------------RYGNENMYQPPIQYFPLG--ICA 118 Gm_GI-356552145.pro P------------------------------------RYGNENMYQPPIQYFPMGSRICA 122 Vv_GI-302142429.pro PQ------------------------HGNGN--------GNGNIYQPIPFFYSTGFRICA 120 Vv_GI-359492104.pro PQ------------------------HGNGN--------GNGNIYQPIPFPYSTGFRICA 123 Sl_GI-460385048.pro PQ------------------------HVSRNDHGGGNVYGNGNFYHPVPFPYSASFRVCA 126 Os_GI-218197709.pro ------------------------------PRARENGNANGGNMYQPLPFMFSSGFRTCA 517 Os_GI-115466772.pro ------------------------------PRARENGNANGGNMYQPLPFMFSSGFRTCA 125 Bd_GI-357160893.pro PCARDNGSPPH---ARDNSSPPHARENSSHPRARENGIANGGNSIQHSPFMFSSGFRTCA 151 Bd_GI-357164660.pro ---------------------PRAREKSSHPRARENGSANGGNSYQL-PLMFSSGFRTCA 133 Sb_GI-242092232.pro P------------------------------PSRENGSANGGNAYHPLPFMFSSGFRACA 125 Zm_GI-212275448.pro PRRNGSAN-------GGTMYHPPRETGNAYQPPRENGSANGGNAYHPLPFMFSSGFRACA 148 At_GI-240256211.pro P------------------------------------RYDPGNILQPYPFLIPSSHPICV 191 At GI-145360806.pro IP------------------------------------------PYEPSYQYRRRQRICG 163 At_GI-22326876.pro IKH-------------------------------SKDHVEE---------EVNPPLSKCK 1241 At_GI-30698242.pro INH-------------------------------SKDVVEE---------DVNPPPS--I 80 At_GI-30698240.pro IQLPDYKILVTSRFEFTSFGPTFHLKPLIDDEVECRDEIEENEKLP----EVNPPLSMCG 348 At_GI-15240018.pro IKQ-------------------------------SKDEVEGDGMLL----ELNPPPSLCG 287 At_GI-334188680.pro IEH-------------------------------FKDPVEEDGNLPRVDLNVNHPHSICD 202 Si_GI-514815267.pro GCKTPIGQGRFLSCMDSVWHPQCFRCYGCDIPISEYEFAVHE---DHAYHRSCYKERF-H 198 Bd_GI-357157184.pro GCNNPIGNGRFLSCMDSVWHPQCFRCFACNKPISEYEFAMHE---NQPYHKSCYKDFF-H 180 Br_DA1b.pro GCNMEIGHGRYLNCIHALWHPQCFRCYGCSHPISEYEFSTSG---NYPFHKACYRERF-H 212 Br_DA1a.pro GCNMEIGHGRYLNCLNALWHPECFRCYGCRHPISEYEFSTSG---NYPFHKACYRERY-H 229 At_GI-15221983.pro GCNMEIGHGRFLNCLNSLWHPECFRCYGCSQPISEYEFSTSG---NYPFHKACYRERY-H 229 Tc_GI-508722773.pro GCNTEIGHGRFLNCLNAFWHPECFRCHACNLPISDYEFSMSG---NYRFHKSCYKERY-H 174 Gm_GI-356564241.pro GCYTEIGFGRYLNCLNAFWHPECFRCRACNLPISDYEFSTSG---NYPYHKSCYKESY-H 174 Gm_GI-356552145.pro GCYTEIGYGRYLNCLNAFWHPECFRCRACNLPISDYEFSTSG---NYPYHKSCYKESY-H 178 Vv_GI-302142429.pro GCNTEIGHGRFLSCMGAVWHPECFRCHGCGYPISDYEYSMNG---NYPYHKSCYKEHY-H 176 Vv_GI-359492104.pro GCNTEIGHGRFLSCMGAVWHPECFRCHGCGYPISDYEYSMNG---NYPYHKSCYKEHY-H 179 Sl_GI-460385048.pro GCSTEIGHGRFLSCMGAVWHPECFRCHACNQPISDYEFSMSG---NYPYHKTCYKEHY-H 182 Os_GI-218197709.pro GCHSEIGHGRFLSCMGAVWHPECFRCHACNQPIYDYEFSMSG---NHPYHKTCYKERF-H 573 Os_GI-115466772.pro GCHSEIGHGRFLSCMGAVWHPECFRCHACNQPIYDYEFSMSG---NHPYHKTCYKERF-H 181 Bd_GI-357160893.pro GCHSEIGHGRFLSCMGAVWHPECFCCHACSQPIYDYEFSMSG---NHPYHKTCYKERF-H 207 Bd_GI-357164660.pro GCHSEIGHGRFLSCMGAVWHPECFCCHGCSQPIYDYEFSMSG---NHPYHKTCYKERF-H 189 Sb_GI-242092232.pro GCHREIGHGRFLSCMGAVWHPECFRCHACSQPIYDYEFSMSG---NHPYHKTCYKEQF-H 181 Zm_GI-212275448.pro GCHREIGHGRFLSCMGAVWHPECFRCHACSQPIYDYEFSMSG---NHPYHKTCYKEQF-H 204 At_GI-240256211.pro GCQAEIGHGRFLSCMGGVWHPECFCCNACDKPIIDYEFSHSG---NRPYHKLCYKEQH-H 247 At GI-145360806.pro GCNSDIGSGNYLGCMGTFFHPECFRCHSCGYAITEHEFSLSG---TKPYHKLCFKELT-H 219 At_GI-22326876.pro DCKSAIEDGISINAYGSVWHPQCFCCLRCREPIAMNEISDLR----GMYHKPCYKELR-H 1296 At_GI-30698242.pro DGKSEIGDGTSVN---------PRCLCCFHCHRPFVMHEILKK---GKFHIDCYKEYYRN 128 At_GI-30698240.pro GCNSAVKHEESVNILGVLWHPGCFCCRSCDKPIAIHELENHVSNSRGKFHKSCYER---- 404 At_GI-15240018.pro GCNFAVEHGGSVNILGVLWHPGCFCCRACHKPIAIHDIENHVSNSRGKFHKSCYER---- 343 At_GI-334188680.pro GCKSAIEYGRSVHALGVNWHPECFCCRYCDKPIAMHEFS----NTKGRCHITCYERSH-- 256 .    :     :        * *: *  *  .:   :            *  *:. Si_GI-514815267.pro PKCDVCNSFIPTNKNGLIEYRAHPFWMQKYCPSHENDGTPRCCSCERMEPKHSQYITLDD 258 Bd_GI-357157184.pro PKCDVCKDFIPTNKDGLIEYRAHPFWMQKYCPSHEDDGTPRCCSCERMEPTDIKYIRLDD 240 Br_DA1b.pro PKCDVCSLFISTNHAGLIEYRAHPFWVQKYCPSHEHDATPRCCSCERMEPRNTGYFELND 272 Br_DA1a.pro PKCDVCSLFIPTNHAGLIGYRAHPFWVQKYCPSHEHDATPRCCSCERMEPRNTGYVELND 289 At_GI-15221983.pro PKCDVCSHFIPTNHAGLIEYRAHPFWVQKYCPSHEHDATPRCCSCERMEPRNTRYVELND 289 Tc_GI-508722773.pro PKCDVCNDFIPTNPAGLIEYRAHPFWIQKYCPSHEHDSTPRCCSCERMEPQDTGYVALND 234 Gm_GI-356564241.pro PKCDVCKHFIPTNPAGLIEYRAHPFWIQKYCPTHEHDGTPRCCSCERMESQEAGYIALKD 234 Gm_GI-356552145.pro PKCDVCKHFIPTNPAGLIEYRAHPFWIQKYCPTHEHDGTTRCCSCERMESQEAGYIALKD 238 Vv_GI-302142429.pro PKCDVCKHFIPTNPAGLIEYRAHPFWVQKYCPSHEHDRTPRCCSCERMEPRDTRYVALND 236 Vv_GI-359492104.pro PKCDVCKHFIPTNPAGLIEYRAHPFWVQKYCPSHEHDRTPRCCSCERMEPRDTRYVALND 239 Sl_GI-460385048.pro PKCDVCKHFIPTNAAGLIEYRAHPFWSQKYCPFHEHDGTPRCCSCERMEPRDTRYIALDD 242 Os_GI-218197709.pro PKCDVCKQFIPTNMNGLIEYRAHPFWLQKYCPSHEVDGTPRCCSCERMEPRESRYVLLDD 633 Os_GI-115466772.pro PKCDVCKQFIPTNMNGLIEYRAHPFWLQKYCPSHEVDGTPRCCSCERMEPRESRYVLLDD 241 Bd_GI-357160893.pro PKCDVCKQFIPTNMNGLIEYRAHPFWLQKYCPSHEVDGTPRCCSCERMEPRESRYVLLDD 267 Bd_GI-357164660.pro PKCDVCQQFIPTNTNGLIEYRAHPFWLQKYCPSHEVDGTPRCCSCERMEPRESRYVLLDD 249 Sb_GI-242092232.pro PKCDVCKQFIPTNMNGLIEYRAHPFWLQKYCPSHEVDGTPRCCSCERMEPRESRYVLLDD 241 Zm_GI-212275448.pro PKCDVCKQFIPTNMNGLIEYRAHPFWVQKYCPSHEMDGTPRCCSCERMEPRESKYVLLDD 264 At_GI-240256211.pro PKCDVCHNFIPTNPAGLIEYRAHPFWMQKYCPSHERDGTPRCCSCERMEPKDTKYLILDD 307 At GI-145360806.pro PKCEVCHHFIPTNDAGLIEYRCHPFWNQKYCPSHEYDKTARCCSCERLESWDVRYYTLED 279 At_GI-22326876.pro PNCYVCEKKIPRTAEGL-KYHEHPFWMETYCPSHDGDGTPKCCSCERLEHCGTQYVMLAD 1355 At_GI-30698242.pro RNCYVCQQKIPVNAEGIRKFSEHPFWKEKYCPIHDEDGTAKCCSCERLEPRGTNYVMLGD 188 At_GI-30698240.pro -YCYVCKEKK------MKTYNIHPFWEERYCPVHEADGTPKCCSCERLEPRGTKYGKLSD 457 At_GI-15240018.pro -YCYVCKEKK------MKTYNNHPFWEERYCPVHEADGTPKCCSCERLEPRESNYVMLAD 396 At_GI-334188680.pro PNCHVCKKKFP-----GRKYKEHPFWKEKYCPFHEVDGTPKCCSCERLEPWGTKYVMLAD 311   * **             :  **** : *** *: * *.:******:*     *  * * Si_GI-514815267.pro GRRLCLECLHTAIMDTNECQPLYIDIQEFYEGMNMKVEQQVPLLLVERQALNEAMEAEKI 318 Bd_GI-357157184.pro GRKLCLECLTSATMDSPECQHLYMDIQEFFEGLNMKVEQQVPLLLVERQALNEALEAEKS 300 Br_DA1b.pro GRKLCLECLDSSVMDTFQCQPLYLQIQEFYEGLNMTVEQEVPLLLVERQALNEAREGERN 332 Br_DA1a.pro GRKLCLECLDSAVMDTFQCQPLYLQIQEFYEGLFMKVEQDVPLLLVERQALNEAREGEKN 349 At_GI-15221983.pro GRKLCLECLDSAVMDTMQCQPLYLQIQNFYEGLNMKVEQEVPLLLVERQALNEAREGEKN 349 Tc_GI-508722773.pro GRKLCLECLDSAVMDTKQCQPLYLDILEFYEGLNMKVEQQVPLLLVERQALNEAREGEKN 294 Gm_GI-356564241.pro GRKLCLECLDSSIMDTNECQPLHADIQRFYDSLNMKLDQQIPLLLVERQALNEAREGEKN 294 Gm_GI-356552145.pro GRKLCLECLDSAIMDTNECQPLHADIQRFYESLNMKLDQQIPLLLVERQALNEAREGEKN 298 Vv_GI-302142429.pro GRKLCLECLDSAIMDTNECQPLYLDIQEFYEGLNMKVQQQVPLLLVERQALNEAMEGEKS 296 Vv_GI-359492104.pro GRKLCLECLDSAIMDTNECQPLYLDIQEFYEGLNMKVQQQVPLLLVERQALNEAMEGEKS 299 Sl_GI-460385048.pro GRKLCLECLDSAIMDTSQCQPLYYDIQEFYEGLNMKVEQKVPLLLVERQALNEAMDGERH 302 Os_GI-218197709.pro GRKLCLECLDSAVMDTSECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKT 693 Os_GI-115466772.pro GRKLCLECLDSAVMDTSECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKT 301 Bd_GI-357160893.pro GRKLCLECLDSAVMDTTECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKT 327 Bd_GI-357164660.pro GRKLCLECLDSAVMDTTECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKT 309 Sb_GI-242092232.pro GRKLCLECLDSAVMDTNECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKA 301 Zm_GI-212275448.pro GRKLCLECLDSAVMDTNDCQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKA 324 At_GI-240256211.pro GRKLCLECLDSAIMDTHECQPLYLEIREFYEGLHMKVEQQIPMLLVERSALNEAMEGEKH 367 At GI-145360806.pro GRSLCLECMETAITDTGECQPLYHAIRDYYEGMYMKLDQQIPMLLVQREALNDAIVGEKN 339 At_GI-22326876.pro FRWLCRECMDSAIMDSDECQPLHFEIREFFEGLHMKIEEEFPVYLVEKNALNKAEKEEKI 1415 At_GI-30698242.pro FRWLCIECMGSAVMDTNEVQPLHFEIREFFEGLFLKVDKEFALLLVEKQALNKAEEEEKI 248 At_GI-30698240.pro GRWLCLECG-KSAMDSDECQPLYFDMRDFFESLNMKIEKEFPLILVRKELLNK--KEEKI 514 At_GI-15240018.pro GRWLCLECMNSAVMDSDECQPLHFDMRDFFEGLNMKIEKEFPFLLVEKQALNKAEKEEKI 456 At_GI-334188680.pro NRWLCVKCMECAVMDTYECQPLHFEIREFFGSLNMKVEKEFPLLLVEKEALKKAEAQEKI 371  * ** :*   :  *: : * *:  :  :: .: :.:::.... **.:. *:.    *:       

SiGI-514815267.pro G-HHLP---ETRGLCLSEEQIVRTILRRPII-GPGNRIIDMITGPYKLVRRCEVTAILIL 373 Bd_GI-357157184.pro G-HHLP---ETRGLCLSEEQIVRTILRRPTI-GPGNRIIDMITGPYKLVRRCEVTAILIL 355 Br_DAlb. pro GHYHMP---ETRGLCLSEEQTVRTVRKRSK----GNWSGNMITEQFKLTRRCEVTAILIL 385 Br_DAla. pro GHYHMP---ETRGLCLSEEQTVSTVRKRSKH-GTGNWAGNMITEPYKLTRQCEVTAILIL 405 At_GI-15221983.pro GHYHMP---ETRGLCLSEEQTVSTVRKRSKH-GTGKWAGN-ITEPYKLTRQCEVTAILIL 404 Tc_GI-508722773.pro GHYHMP---ETRGLCLSEEQTVSTILRQPRF-GTGNRAMDMITEPCKLTRRCEVTAILIL 350 Gm_GI-356564241.pro GHYHMP---ETRGLCLSEE--LSTFSRRPRL-G---TAMDMRAQPYRPTTRCDVTAILVL 345 Gm_GI-356552145.pro GHYHMP---ETRGLCLSEE--LSTFSRRPRL-G---TTMDMRAQPYRPTTRCDVTAILIL 349 Vv_GI-302142429.pro GHHHMP---ETRGLCLSEEQTVSTILRRPKI-GTGNRVMNMITEPCKLTRRCDVTAVLIL 352 Vv_GI-359492104.pro GHHHMP---ETRGLCLSEEQTVSTILRRPKI-GTGNRVMNMITEPCKLTRRCDVTAVLIL 355 Sl_GI-460385048 .pro GYHHMP---ETRGLCLSEEQTISTIQRRPRI-GAGNRVMDMRTEPYKLTRRCEVTAILIL 358 Os_GI-218197709 .pro GHHHLP---ETRGLCLSEEQTVSTILRRPRM-AGN-KVMEMITEPYRLTRRCEVTAILIL 748 OsGI-115466772.pro GHHHLP---ETRGLCLSEEQTVSTILRRPRM-AGN-KVMEMITEPYRLTRRCEVTAILIL 356 Bd_GI-357160893.pro GHHHLP---ETRGLCLSEEQTVSTILRRPRM-TGN-KIMEMITEPYRLTRRCEVTAILIL 382 Bd_GI-357164660.pro GHHHLP---ETRGLCLSEEQTVSTILRRPRM-AGN-KIMEMRTEPYRLTRRCEVTAILIL 364 Sb_GI-242092232.pro GHHHLP---ETRGLCLSEEQTVSTILRRPRM-AGN-KIMGMITEPYRLTRRCEVTAILIL 356 Zm_GI-212275448.pro GHHHLP---ETRGLCLSEEQTVSTILR-PRM-AGN-KIMGMITEPYRLTRRCEVTAILIL 378 At_GI-240256211.pro GHHHLP---ETRGLCLSEEQTVTTVLRRPRI-GAGYKLIDMITEPCRLIRRCEVTAILIL 423 At_GI-145360806.pro GYHHMP---ETRGLCLSEEQTVTSVLRRPRL-G-AHRLVGMRTQPQRLTRKCEVTAILVL 394 At_GI-22326876.pro DKQGDQCLMVVRGICLSEEQIVTSVSQGVRR-MLNKQILDTVTESQRVVRKCEVTAILIL 1474 At_GI-30698242.pro DYHR---AAVTRGLCMSEEQIVPSIIKGPRMGPDNQLITDIVTESQRVS-GFEVTGILII 304 At_GI-30698240.pro DNHY---EVLIRAYCMSEQKIMTYVSEEPRT-GQNKQLIDMDTEPQGVVHECKVTAILIL 570 At_GI-15240018.pro DYQY---EVVTRGICLSEEQIVDSVSQRPVR-GPNNKLVGMATESQKVTRECEVTAILIL 512 At_GI-334188680.pro DNQH---GVVTRGICLSEGQIVNSVFKKPTM-GPNGELVSLGTEPQKVVGGCEVTAILIL 427 SiGI-514815267.pro YGLPRLLTGSILAHEMMHAYLRLK---------------------------GYRTLSPEV 406 Bd_GI-357157184.pro YGLPRLQTGSILAHEMMHAYLRLK---------------------------GYRSLSPQV 388 Br_DAlb. pro FGLPRLLTGSILAHEMMHAWMRLK---------------------------GFRPLSQDV 418 Br_DAla. pro FGLPRLLTGSILAHEMMHAWMRLK---------------------------GFRTLSQDV 438 At_GI-15221983.pro FGLPRLLTGSILAHEMMHAWMRLK---------------------------GFRTLSQDV 437 Tc_GI-508722773.pro YGLPRLLTGSILAHEMMHAWMRLQ---------------------------GFRTLSQDV 383 Gm_GI-356564241.pro YGLPRLLTGSILAHEMMHAWLRLK---------------------------GYRTLSQDV 378 Gm_GI-356552145.pro YGLPRLLTGSILAHEMMHAWLRLK---------------------------GYRTLSQDV 382 Vv_GI-302142429.pro YGLPRLLTGSILAHEMMHAWLRLN---------------------------GYRTLAQDV 385 Vv_GI-359492104.pro YGLPRLLTGSILAHEMMHAWLRLN---------------------------GYRTLAQDV 388 Sl_GI-460385048 .pro YGLPRLLTGSILAHEMMHAWLRLR---------------------------GYRTLSQDV 391 Os_GI-218197709 .pro YGLPRLLTGSILAHEMMHAWLRLK---------------------------GYRTLSPDV 781 OsGI-115466772.pro YGLPRLLTGSILAHEMMHAWLRLK---------------------------GYRTLSPDV 389 Bd_GI-357160893.pro YGLPRLLTGSILAHEMMHAWLRLK---------------------------GYRTLSPEI 415 Bd_GI-357164660.pro YGLPRLLTGSILAHEMMHAWLRLK---------------------------GYRTLSPDI 397 Sb_GI-242092232.pro YGLPRLLTGSILAHEMMHAWLRLK---------------------------GYRTLSPDV 389 Zm_GI-212275448.pro YGLPRLLTGSILAHEMMHAWLRLK---------------------------GYRTLSPDV 411 At_GI-240256211.pro YGLPRLLTGSILAHEMMHAWLRLN --------------------------GYPNLRPEV 456 At_GI-145360806.pro YGLPRLLTGAILAHELMHGWLRLN---------------------------GFRNLNPEV 427 At_GI-22326876.pro YGLPRLLTGYILAHEMMHAYLRLN---------------------------GYRNLNMVL 1507 At_GI-30698242.pro YGLPRLLTGYILAHEMMHAWLRLN---------------------------GYKNLKLEL 337 At_GI-30698240.pro YGLPRLLTGYILAHEMMHAWLRLN---------------------------GHMNLNNIL 603 At_GI-15240018.pro YGLPRLLTGYILAHEMMHAYLRLN---------------------------GHRNLNNIL 545 At_GI-334188680.pro YGLPRLLTGYILAHEMMHAWLRLNGTTSTQFVFANQYGESSQLKVLFGLITGYRNLKLEL 487 :***** ** *****:**.::**.                           *.  *   : SiGI-514815267.pro EEGICQVLAHLWLESEITSGSGSMATTSAASSS-----SSTS--SSSKKGA-KTEFEKRL 458 Bd_GI-357157184.pro EEGICQVLSHMWLESEIIAGASGNTASTSVPSS-----SSAP--TSSKKGA-KTEFEKRL 440 Br_DAlb. pro EEGICQVMAHKWLEAELAAGSRNSNAASSSSSS-----Y-----GGVKKGP-RSQYERKL 467 Br_DAla. pro EEGICQVMAHKWLEAELAAGSRNSNVASSSS-------------RGVKKGP-RSQYERKL 485 At_GI-15221983.pro EEGICQVMAHKWLDAELAAGSTNSNAASSSSSS-----------QGLKKGP-RSQYERKL 485 Tc_GI-508722773.pro EEGICQVLAHMWLLTQLEYAS-SSNVASASSSA-----S-----SRLQKGK-RPQFEGKL 431 Gm_GI-356564241.pro EEGICQVLAHMWLESELSSASGSNFVSASSSSA-----S-----HTSRKGK-RPQFERKL 427 Gm_GI-356552145.pro EEGICQVLSHMWLESELSSASGSNFVSASSSSA-----S-----HTSRKGK-RPQFERKL 431 Vv_GI-302142429.pro EEGICQVLAYMWLDAELTSGSGR------------------------------SQCERKL 415 Vv_GI-359492104.pro EEGICQVLAYMWLDAELTSGSGSNV-PSTSSAS-----------TSSKKGA-GSQCERKL 435 Sl_GI-460385048 .pro EEGICQVLAHMWLETQIASISSSNGGASTSSGM-----------SSSKQGI-RSPFERKL 439 Os_GI-218197709 .pro EEGICQVLAHMWIESEIIAGSGSNGASTSSSSS-----AS----TSSKKGG-RSQFERKL 831 OsGI-115466772.pro EEGICQVLAHMWIESEIIAGSGSNGASTSSSSS-----AS----TSSKKGG-RSQFERKL 439 Bd_GI-357160893.pro EEGICQVLAHMWIESEIMAGSSSNAASTSSSSS-----SS----ISSKKGG-RSQFERKL 465 Bd_GI-357164660.pro EEGICQVLAHMWIESEITAGSGSNAASTSSSST-----S-------SKKGG-RSQFERKL 444 Sb_GI-242092232.pro EEGICQVLAHLWIESEIMAGSGSGAASSSSGSS-----SS----MSSKKAG-RSQFEHKL 439 Zm_GI-212275448.pro EEGICQVLAHMWIESEIMAGSGSSAASSSSGSS-----SS----TSSKKGG-RSQFEHRL 461 At_GI-240256211.pro EEGICQVLAHMWLESETYAGSTLVDIASSSSSA-----VVS---ASSKKGE-RSDFEKKL 507 At_GI-145360806.pro EEGICQVLSYMWLESEVLSDPSTRNLPSTSSVA-----TSSSSSFSNKKGG-KSNVEKKL 481 At_GI-22326876.pro EEGLCQVLGYMWLECQTYVFD----TATIASSS--SSSRTPLSTTTSKKVD-PSDFEKRL 1560 At_GI-30698242.pro EEGLCQALGLRWLESQTFASTDAAAAAAVASSSSFSSSTAPPAAITSKKSDDWSIFEKKL 397 At_GI-30698240.pro EEGICQVLGHLWLESQTYATADTTADAASASSS---SSRTPPAASASKKGE-WSKFDKKL 659 At_GI-15240018.pro EEGICQVLGHLWLDSQTYATADATADASSSASS---SSRTPPAASASKKGE-WSDFDKKL 601 At_GI-334188680.pro EEGICQVLGHMWLESQTYS----SSAAASSASS---SSRTP-AANASKKGA-QSDYEKKL 538 ***:**.:.  *:  :                                     .  : :*   Si_GI-514815267 .pro GEFFKHQIETDPSVAYGDGFRAGMRAVERYG--LRSTLDHIKLTGSFP----- 504 Bd_GI-357157184 .pro GAFIKNQIETDSSVEYGDGFRAGNRAVERYG--LRSTLDHMKITGSFPY---- 487 Br_DA1b . pro GEFFKHQIESDASPVYGDGFRAGRLAVNKYG--LWRTLEHIQMTGRFPV---- 514 Br_DAla . pro GEFFKHQIESDASPVYGDGFRAGRLAVNKYG--LPKTLEHIQMTGRFPV---- 532 At_GI-15221983.pro GEFFKHQIESDASPVYGDGFRAGRLAVHKYG--LRKTLEHIQMTGRFPV---- 532 Tc_GI-508722773.pro GEFFKHQIESDTSPVYGDGFRAGHQAVYKYG--LRRTLEHIRMTGRFPY---- 478 Gm_GI-356564241.pro GEFFKHQIESDISPVYGDGFRAGQKAVRKYG--LQRTLHHIRMTGTFPY---- 474 Gm_GI-356552145.pro GEFFKHQIESDISPVYGGGFRAGQKAVSKYG--LQRTLHHIRMTGTFPY---- 478 Vv_GI-302142429.pro GQFFKHQIESDTSLVYGAGFRAGHQAVLKYG--LPATLKHIHLTGNFPY---- 462 Vv_GI-359492104.pro GQFFKHQIESDTSLVYGAGFRAGHQAVLKYG--LPATLKHIHLTGNFPY---- 482 Sl_GI-460385048.pro GDFFKHQIESDTSPIYGNGFRAGNQAVLKYG--LERTLDHIRMTGTFPY---- 486 Os_GI-218197709.pro GDFFKHQIESDTSMAYGDGFRAGNRAVLQYG--LKRTLEHIRLTGTFPF---- 878 Os_GI-115466772.pro GDFFKHQIESDTSMAYGDGFRAGNRAVLQYG--LKRTLEHIRLTGTFPF---- 486 Bd_GI-357160893.pro GDFFKHQIESDTSVAYGNGFRSGNQAVLQYG--LKRTLEHIWLTGTWPF---- 512 Bd_GI-357164660.pro GDFFKHQIESDTSVAYGDGFRAGNQAVLQYG--LKRTLEHIRLTGTLPF---- 491 Sb_GI-242092232.pro GDFFKHQIETDTSMAYGEGFRAGNRAVLQYG--LKRTLEHIRLTGTFPF---- 486 Zm_GI-212275448.pro GDFFKHQIETDTSMAYGDGFRTGNRAVLHYG--LKRTLEHIRLTGTFPF---- 508 At_GI-240256211.pro GEFFKHQIESDSSSAYGDGFRQGNQAVLKHG--LRRTLDHIRLTGTFP----- 553 At_GI-145360806.pro GEFFKHQIAHDASPAYGGGFRAANAAACKYG--LRRTLDHIRLTGTFPL---- 528 At_GI-22326876.pro VNFCKHQIETDESPFFGDGFRKVNKMMASNNHSLKDTLKEIISISKTPQYSKL 1613 At_GI-30698242.pro VEFCMNQIKEDDSPVYGLGFKQVYEMMVSNNYNIKDTLKDIVSASNATPDSTV 450 At_GI-30698240.pro VEFCKNQIETDESPVYGLGFRTVNEMVTNS--SLQETLKEILRRR-------- 702 At_GI-15240018.pro VEFCKNQIETDDSPVYGLGFRTVNEMVTNS--SLQETLKEILRQR-------- 644 At_GI-334188680.pro VEFCKDQIETDDSPVYGVGFRKVNQMVSDS--SLHKILKSIQHWTKPDSNL-- 587

TABLE 4 Alignment of EODI proteins (SEQ ID NOS: 74-90) Zm_GI-223973923.pro ----------------------MNSS--RQMELHYINTGFPYTITESFMDFFEGLTYAHA 36 Sb_GI-242042045.pro ----------------------MNSC--RQMELHYINTGFPYTITESFMDFFEGLTYAHA 36 Zm_GI-226496789.pro ----------------------MTSS--RQMELHYINTGFPYTITESFMDFFEGLTYAHA 36 Os_GI-222624282.pro MTESHERDTEVTRWQVHDPSEGMNGS--RQMELHYINTGFPYTITESFMDFFEGLTYAHA 58 Os_GI-115451045.pro ----------------------MNGS--RQMELHYINTGFPYTITESFMDFFEGLTYAHA 36 Bd_GI-357113826.pro ----------------------MNGS--RQMELHYINTGFPYTITESFMDFFEGLTYAHA 36 Sl_GI-460410949.pro ----------------------MNWN--QQTEIYYTNGAMPYNSIGSFMDFFGGVTYDHV 36 Rc_GI-255582236.pro ------------------------------MEVHYINTGFPYTVTESFLDFFEGLSHVPV 30 Pt_GI-224059640.pro ------------------------------MEVHYMNTDFPYTTTESFMDFFEGLTHAPV 30 Gm_GI-356548935.pro ----------------------MNDG--RQMGVHYVDAGFPYAVNDNFVDFFQGFTHVPV 36 Gm_GI-356544176.pro ----------------------MNDG--RQMGVNYVDAGFPYAVNENFVDFFQGFTPVPV 36 Vv_GI-359487286.pro ----------------------MNGN--RQMEVHYINTGFPYTITESFMDFFEGLGHVPV 36 Tc_GI-508704801.pro ----------------------MNGN--RQMEVHYIDTGFPYTATESFMDFFEGLTHVPV 36 Pp_GI-462414664.pro ----------------------MNGN--GQMDVHYIDTDFPYTPTESFMDFFGGVTHVPM 36 Cr_GI-482561003.pro ----------------------MNGD-RPVEDAHYTEAEFPYAASGSYIDFYGGAPQGPL 37 At_GI-22331928.pro ----------------------MNGDNRPVEDAHYTETGFPYAATGSYMDFYGGAAQGPL 38 Sl_GI-460370551.pro ----------------------MSGD-QHMEAMHYMNMGFPYNVPESFPGFLDGVSQAPI 37                                   * :  :**    .: .*  * Zm_GI-223973923.pro DFALTDGFQDQ--GNPYWAMMHTNSYKYGYSGPG--NYYSYAHVYDIDDYMRRADGGRRI 92 Sb_GI-242042045.pro DFALMDGFQDQ--GNPYWAMMHTNSYKYGYSGPG--NYYTYAHVYDIDDYMHRADGGRRV 92 Zm_GI-226496789.pro DFALMDGFQDQ--GNPYWTMMHTNSYKYGYSGSG--NYYSYAHAYDIDDYMHRTDGGRRT 92 Os_GI-222624282.pro DFAIADAFHDQ--ANPYWAMMHTNSYKYGYSGAG--NYYSYGHVYDMNDYMHRADGGRRI 114 Os_GI-115451045.pro DFAIADAFHDQ--ANPYWAMMHTNSYKYGYSGAG--NYYSYGHVYDMNDYMHRADGGRRI 92 Bd_GI-357113826.pro DFALADAFQDQ--ANPYWTMMQTNSYKYGYSGAS--NYYSYGHVYDMNDYMHRADGGRRI 92 Sl_GI-460410949.pro NYIFADPPYAQ--ES-LYPSISTNPYKFGYSEAGSFSYYDYDREYVVNDHVSGIEEHDRH 93 Rc_GI-255582236.pro HYAHTGQVLDQ-VQENAYWSMNMNAYKYGFSGPGST-YYDP---YEVNDNLPRMDVSRST 85 Pt_GI-224059640.pro NYAHNGPMHD---QDNAYWSMNMNAYKFGFSGLGSTSYYSP---YEVNDNLPRMDVSRMA 84 Gm_GI-356548935.pro NYAFAGSIPDQ---ESVYWSMNMNPYKFGLSGPGSTSYYSS---YEVNGHLPRMEIDRAE 90 Gm_GI-356544176.pro NYAFAGSIPDQ---ESVYWSMNMNPYKFGLSGPGSTSYYSS---YEVNGHLPRMEIDRAE 90 Vv_GI-359487286.pro NYAQAEAMHNQSIQENFYWTMNMNSYKFGFSGPGST-YYGP---YDVNEHVPGIEVSRRP 92 Tc_GI-508704801.pro NYTHTVPMQDQ---ENIYWSMSMNAYKFGFSGPEST-FYSP---YEVSDHLPRMDVSRRT 89 Pp_GI-462414664.pro NYGHAMPMHDQ---ETAYWSMNMHSYKFGPSGPGSNSYYGNY--YEVNDHLPRMDVSRRT 91 Cr_GI-482561003.pro NYAHAGTM------DNLYWTMNTNAYKFGFSGSDNPSFYNS---YDMTDHLSRMSIGRTN 88 At_GI-22331928.pro NYDHAATMHPQ---DNLYWTMNTNAYKFGFSGSDNASFYGS---YDMNDHLSRMSIGRTN 92 Sl_GI-460370551.pro IQYHNNPVQIQ-DQENAYWSMNMSYYKYEHSNLESTSYHSY---ETGNNHVSRPDFSERP 93               .  :  :    **:  *      ::           :   . Zm_GI-223973923.pro WDNTTPVNNVDSANVVLQGG-EAPHTTTNTINKECIQQ-VHQSPGSPQVVWQDNIEPDNM 150 Sb_GI-242042045.pro WDNTTPANNVDSANVVLQGS-EAPRTTANTTTEECIQQ-VHQSPGSPHVVWQDNIDPDNM 150 Zm_GI-226496789.pro WDNTTPVNNVDSANVVLQGG-EAPRTTANTTSEDCIQQ-VHQSPGSPQVVWQDNIDPDNM 150 Os_GI-222624282.pro WDNATPVNNTESPNVVLQGG-ETPHANTSSTTEECIQQQVHQNSSSPQVIWQDNIDPDNM 173 Os_GI-115451045.pro WDNATPVNNTESPNVVLQGG-ETPHANTSSTTEECIQQQVHQNSSSPQVIWQDNIDPDNM 151 Bd_GI-357113826.pro WDNPTPASNTDSPNVVLQGAAEAPHPRASSTTEECIQQPVHQNSSSPQVVWQDNVDPDNM 152 Sl_GI-460410949.pro LENPSTTTVNVAANVHRE---EISGSNSLTNSVECPRG--QINTRDSEVVWQDNIDPDNM 148 Rc_GI-255582236.pro WEYPSVVMMEEA-TTTDTQSEGDAVVGVHASPEECIPN-HT-SGDSPQGVWQDDVDPDNM 142 Pt_GI-224059640.pro WEYPSVV---------------------------------------IKALWQDDVDPDTM 105 Gm_GI-356548935.pro WEYPSTITTVEEPATTDSPPRRDGVTSMQTIPEECSPN-HHESNSSSQVIWQDNIYPDDM 149 Gm_GI-356544176.pro WEYPSTITTVEEPATTDSPPRRDGVTNMQTIPEECSPN-HHESNSSSQVIWQDNIDPDNM 149 Vv_GI-359487286.pro WEYPSSM-IVEEPTTIETQPTGNEVMNVHAIPEECSPN-HY-SATSSQAIWQDNVDPDNM 149 Tc_GI-508704801.pro WDYPSTL-NSEEPATIDMQPGGEAVVGIHAIPEECITN-HQ-SNSNSQVVWQDNIDPDNM 146 Pp_GI-462414664.pro WEHPSVM-NSEEPANIDSHPEEEDAVA-EAAPEECIQN-QQ-NTNTSQVVWQEDIDPDNM 147 Cr_GI-482561003.pro WEYHPMVNVDD-PDITLARSVQIGDSDEHSEAEDCIAN--EHDPDSPQVSWQDDIDPDTM 145 At_GI-22331928.pro WDYHPMVAVADDPENTVARSVQIGDTDEHSEAEECIAN--EHDPDSPQVSWQDDIDPDTM 180 Sl_GI-460370551.pro WEYAVPMNVHEG-VSTDVIYEENTVPVEDVGTEECVLS--NQDDSNHQDILEDEIDLDNM 150 Zm_GI-223973923.pro TYEELLDLGEAVGTQSRGLSQERISSLPVTKYKCG-FFSRKKTRRERCVICQMEYRRGNL 309 Sb_GI-242042045.pro TYEELLDLGEVVGTQSRGLSQERISSLPVEKYKCG-FFSRKKTRRERCVICQMEYRRGNL 209 Zm_GI-226496789.pro TYEELLDLGEAVGTQSRGLSQECISLLPITKYKCG-FFSRKKTRRERCVICQMEYRRGNL 209 Os_GI-222624282.pro TYEELLDLGEAVGTQSRGLSQERISLLPVTKYKCG-FFSRKKTRRERCVICQMEYRRGNL 232 Os_GI-115451045.pro TYEELLDLGEAVGTQSRGLSQERISLLPVTKYKCG-FFSRKKTRRERCVICQMEYRRGNL 210 Bd_GI-357113826.pro TYEELLDLGEAVGTQSRGLSQERISSLPVTKYKCG-FFSRKKTRRERCVICQMEYRRGDL 211 Sl_GI-460410949.pro TYEELLELGEAVGTQSRGLSQNQISLLPVTKFKCG-FFSRKKSRKERCVICQMEYKRKDQ 207 Rc_GI-255582236.pro TYEELLDLGETVGTQSRGLSQELISLLPTSKCKFRSFFLRKKAG-ERCVICQMRYKRGDK 201 Pt_GI-224059640.pro TYEELVDLGETVGTQSKGLSPELISLLPTSKCKPGSFPSRKRSG-ERCVICQMKYKRGDK 164 Gm_GI-356548935.pro TYEELLDLGEAVGTQSRGLSQELIDMLPTSKYKFGSLFKRKNSG-ERCVICQMTYRRGDQ 208 Gm_GI-356544176.pro TYEELLDLGEAVGTQSRGLSQELIDMLPTSKYKFGNLFKRKNSG-KRCVICQMTYRRGDQ 208 Vv_GI-359487286.pro TYEELLDLGEAVGTQSRGLSQEHINLLPTCRYKSGRLFSRKRSA-ERCVICQMGYKRGDR 208 Tc_GI-508704801.pro TYEELLDLGETIGSQSRGLSQELIDLLPTSKCKFGSFFSTKR---ERCVICQMRYKRGEQ 203 Pp_GI-462414664.pro TYEELLDLGEAVGTQSRGLSDELISLLPTSKYKCGSFFSRKKSG-ERCVICQMRYKRGDR 206 Cr_GI-482561003.pro TYEELVELGEAVGTESRGLSQELIEELPTRKFKFGSIFSRKRAG-ERCVICQLKYKIGER 204 At_GI-22331928.pro TYEELVELGEAVGTESRGLSQELIETLPTEKYKFGSIFSRKRAG-ERCVICQLKYKIGER 209 Sl_GI-460370551.pro TYEELLDLGETVGTESRGLAEELINLLPTTKYKSNGIFSRKKSE-ERCVICQMRYKRGDR 209 *****::***.:*::*:**: : *. **  : *   :*  *.   :******: *:  : Zm_GI-223973923.pro QMTLPCKHVYHASCVTRWLGINKVCPVCFAEVPGEDPEAMSQQL 253 Sb_GI-242042045.pro QMTLPCKHVYHASGVTRWLSINKVCPVCFAEVPGDEPKRQ---- 249 Zm_GI-226496789.pro QITLPCKHVYHASCVTRWLSINKVCPVCFAEVPGEDSLRQ---- 249 Os_GI-222624282.pro QMTLPCKHVYHASCVTRWLSINKVCPVCFAEVPGDEPKRQ---- 272 Os_GI-115451045.pro QMTLPCKHVYHASCVTRWLSINKVCPVCFAEVPGDEPKRQ---- 250 Bd_GI-357113826.pro QMALPCKHVYHASCVTRWLSINKVCPVCFAEVPSEEPSRQ---- 251 Sl_GI-460410949.pro QVTLPCKHVYHAGCGSRWLSINKACPICKTEVVINTSKR----- 246 Rc_GI-255582236.pro QMKLPCKHVYHSECISKWLGINKVCPVCNNEVFGEDSRH----- 240 Pt_GI-224059640.pro QIKLLCKHAYHSECITKWLGINKVCPVCNDEVFGEESRN----- 203 Gm_GI-356548935.pro QMKLPCSHVYHGECITKWLSINKKCPVCNTEVFGEESTH----- 247 Gm_GI-356544176.pro QMKLPCSHVYHGECITKWLSINKECPVCNTEVFGKESTH----- 247 Vv_GI-359487286.pro QIKLPCKHVYHTDCGTKWLTINKVCPVCNIEVFGEESRH----- 247 Tc_GI-508704801.pro QMKLPCKHVYHSQCITKWLSINKICPVCNNEVFGEESRH----- 242 Pp_GI-462414664.pro QINLPCKHVYHSECISKWLGINKVCEVCNLEVSGEESRH----- 245 Cr_GI-482561003.pro QMNLPCKHVYHSECISKWLSINKVCPVCNTEVFGDPSIH----- 243 At_GI-22331928.pro QMNLPCKHVYHSECISKWLSINKVCPVCNSEVFGEPSIH----- 248 Sl_GI-460370551.pro QINFPCKHIYHTECGSKWLSINKRCSLMNEVVQW---------- 243 *: : *.* **  * ::** *** *.:    * 

What is claimed is:
 1. A plant, or a plant cell thereof, comprising a mutation that reduces the expression or activity of a DA2 polypeptide, wherein the plant has increased seed size and/or organ size relative to a plant without the mutation.
 2. The plant of claim 1, wherein the DA2 polypeptide comprises an amino acid sequence having at least 90% sequence identity to one or more of SEQ ID NOs: 20 to
 35. 3. The plant of claim 1, wherein the mutation abolishes the expression or activity of the DA2 polypeptide.
 4. The plant of claim 1, wherein the mutation is in the nucleotide sequence that encodes the DA2 polypeptide or that regulates its expression.
 5. The plant of claim 1, wherein the DA2 polypeptide comprises a RING domain of SEQ ID NO:
 1. 6. The plant of claim 1, wherein the DA2 polypeptide comprises a RING domain of SEQ ID NO:
 2. 7. The plant of claim 1, wherein the DA2 polypeptide comprises a first consensus domain of SEQ ID NO:
 36. 8. The plant of claim 1, wherein the DA2 polypeptide comprises a second consensus domain of SEQ ID NO:
 37. 9. The plant of claim 1, wherein the plant is a monocotyledonous or dicotyledonous plant.
 10. The plant of claim 1, wherein the plant is an agricultural plant selected from the group consisting of Lithospermum erythrorhizon, Taxus spp, tobacco, cucurbits, carrot, vegetable brassica, melons, capsicums, grape vines, lettuce, strawberry, oilseed brassica, sugar beet, wheat, barley, maize, rice, soyabeans, peas, sorghum, sunflower, tomato, potato, pepper, chrysanthemum, carnation, linseed, hemp and rye.
 11. The plant of claim 1, wherein the plant is maize.
 12. The plant of claim 1, wherein the plant is not Arabidopsis thaliana.
 13. A maize plant, or a maize plant cell thereof, comprising a mutation that reduces the expression or activity of a DA2 polypeptide, wherein the maize plant has increased seed size and/or organ size relative to a maize plant without the mutation.
 14. The maize plant of claim 13, wherein the DA2 polypeptide comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 30 or
 34. 15. The maize plant of claim 13, wherein the mutation abolishes the expression or activity of the DA2 polypeptide.
 16. The maize plant of claim 13, wherein the mutation is in the nucleotide sequence that encodes the DA2 polypeptide or that regulates its expression.
 17. The maize plant of claim 13, wherein the DA2 polypeptide comprises a RING domain of SEQ ID NO:
 1. 18. A method of increasing the seed size and/or organ size of a plant, the method comprising: introducing within cells of the plant a mutation that reduces the expression or activity of a DA2 polypeptide.
 19. The method of claim 18, wherein the DA2 polypeptide comprises an amino acid sequence having at least 90% sequence identity to one or more of SEQ ID NOs: 20 to
 35. 20. The method of claim 18, wherein the plant is maize. 